MOMENTA PHARMACEUTICALS, INC.
675 West Kendall Street
Cambridge, Massachusetts 02142

May 7, 2008

To Our Stockholders:

        You are cordially invited to attend the 2008 Annual Meeting of Stockholders of Momenta Pharmaceuticals, Inc. to be held at 10:00 a.m., local time, on Wednesday, June 4, 2008, at the offices of Wilmer Cutler Pickering Hale and Dorr LLP, 60 State Street, Boston, Massachusetts 02109.

        The Notice of Meeting and Proxy Statement on the following pages describe the matters to be presented at the meeting.

        It is important that your shares be represented at this meeting to assure the presence of a quorum. Whether or not you plan to attend the meeting, we hope that you will have your stock represented by voting your shares over the Internet or by telephone as provided in the instructions set forth on the enclosed proxy card, or by completing, signing, dating and returning your proxy in the enclosed envelope, as soon as possible. Your stock will be voted in accordance with the instructions you have given in your proxy.

        Thank you for your continued support.

Sincerely,



Craig A. Wheeler
President and Chief Executive Officer

MOMENTA PHARMACEUTICALS, INC.
675 West Kendall Street
Cambridge, Massachusetts 02142

NOTICE OF 2008 ANNUAL MEETING OF STOCKHOLDERS

To Be Held On June 4, 2008

To Our Stockholders:

        NOTICE IS HEREBY GIVEN that the 2008 Annual Meeting of Stockholders of Momenta Pharmaceuticals, Inc., or the Annual Meeting, will be held on Wednesday, June 4, 2008 at 10:00 a.m., local time, at the offices of Wilmer Cutler Pickering Hale and Dorr LLP, 60 State Street, Boston, Massachusetts 02109. At the Annual Meeting, stockholders will consider and vote on the following matters:

1.

The election of three (3) members to our board of directors to serve as Class I directors, each for a term of three years; and



2.

The ratification of the selection by the Audit Committee of our board of directors of Ernst & Young LLP as our independent registered public accounting firm for the year ending December 31, 2008.

        The stockholders will also act on any other business that may properly come before the Annual Meeting or any adjournment thereof.

        Stockholders of record at the close of business on Monday, April 14, 2008 are entitled to notice of, and to vote at, the Annual Meeting or any adjournment thereof. Your vote is important regardless of the number of shares you own. A complete list of such stockholders will be open to the examination of any stockholder at our principal executive offices at 675 West Kendall Street, Cambridge, Massachusetts 02142, during ordinary business hours, for a period of ten days prior to the Annual Meeting as well as on the day of the Annual Meeting. The Annual Meeting may be adjourned from time to time without notice other than by announcement at the Annual Meeting.

        We hope that all stockholders will be able to attend the Annual Meeting in person. However, to ensure that a quorum is present at the Annual Meeting, please vote your shares over the Internet or by telephone as provided in the instructions set forth on the enclosed proxy card, or complete date, sign and promptly return the enclosed proxy card whether or not you expect to attend the Annual Meeting. A postage-prepaid envelope, addressed to Broadridge Financial Solutions, serving as proxy tabulator, has been enclosed for your convenience. If you attend the Annual Meeting in person, your proxy will, upon your written request, be returned to you and you may vote your shares in person.

        All stockholders are cordially invited to attend the Annual Meeting.

By Order of the Board of Directors,



Craig A. Wheeler
President and Chief Executive Officer

Cambridge, Massachusetts
May 7, 2008

WHETHER OR NOT YOU EXPECT TO ATTEND THE ANNUAL MEETING, PLEASE VOTE YOUR SHARES OVER THE INTERNET OR BY TELEPHONE AS PROVIDED IN THE INSTRUCTIONS SET FORTH ON THE ENCLOSED PROXY CARD, OR COMPLETE, DATE AND SIGN THE ENCLOSED PROXY CARD AND PROMPTLY MAIL IT IN THE ENCLOSED ENVELOPE TO ASSURE REPRESENTATION OF YOUR SHARES AT THE ANNUAL MEETING. NO POSTAGE NEED BE AFFIXED IF THE PROXY CARD IS MAILED WITHIN THE UNITED STATES.

MOMENTA PHARMACEUTICALS, INC.
675 WEST KENDALL STREET
CAMBRIDGE, MASSACHUSETTS 02142

PROXY STATEMENT

for the 2008 Annual Meeting of Stockholders
to be held on Wednesday, June 4, 2008

        This proxy statement and the enclosed proxy card are being furnished in connection with the solicitation of proxies by the board of directors of Momenta Pharmaceuticals, Inc., also referred to in this proxy statement as the "Company", "Momenta", "we" or "us", for use at the 2008 Annual Meeting of Stockholders, or the Annual Meeting, to be held on Wednesday, June 4, 2008 at 10:00 a.m., local time, at the offices of Wilmer Cutler Pickering Hale and Dorr LLP, 60 State Street, Boston, Massachusetts 02109, and at any adjournment thereof. You may obtain directions to the location of the Annual Meeting by contacting Steven N. Avruch, Esq., Corporate Secretary, Momenta Pharmaceuticals, Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142; telephone: (617) 491-9700.

        All proxies will be voted in accordance with the instructions contained in those proxies. If no choice is specified, the proxies will be voted in favor of the matters set forth in the accompanying Notice of Meeting. Any proxy may be revoked by a stockholder at any time before it is exercised by delivery of written revocation to our corporate secretary or by appearing at the Annual Meeting and voting in person.

        Our 2007 Annual Report to Stockholders for the fiscal year ended December 31, 2007 is being mailed to stockholders with the mailing of these proxy materials on or about May 7, 2008.

Important Notice Regarding the Availability of Proxy Materials for the Annual
Meeting of Stockholders to be Held on June 4, 2008:

        This proxy statement and the 2007 Annual Report to Stockholders are available for viewing, printing and downloading at http://ir.momentapharma.com/financials.cfm.

        A copy of our Annual Report on Form 10-K for the fiscal year ended December 31, 2007 as filed with the Securities and Exchange Commission, except for exhibits, will be furnished without charge to any stockholder upon written request to Momenta Pharmaceuticals, Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142, Attention: Richard P. Shea, Chief Financial Officer and Treasurer, telephone: (617) 491-9700.

Voting Securities and Votes Required

        Stockholders of record at the close of business on Monday, April 14, 2008 will be entitled to notice of, and to vote at, the Annual Meeting. On that date, 36,772,829 shares of our common stock were issued and outstanding. Each share of common stock entitles the holder thereof to one vote with respect to all matters submitted to stockholders at the Annual Meeting. We have no other securities entitled to vote at the Annual Meeting.

        The presence in person or representation by proxy of the holders of a majority of the shares of common stock issued and outstanding and entitled to vote at the Annual Meeting is necessary to establish a quorum for the transaction of business. If a quorum is not present, the Annual Meeting will be adjourned until a quorum is obtained.

        Directors are elected by a plurality of the votes cast by the stockholders entitled to vote on the election. To be approved, any other matter submitted to our stockholders, including the ratification of the appointment of Ernst & Young LLP as our independent registered public accounting firm, requires the affirmative vote of a majority in voting power of the outstanding shares of stock present or represented and voting on such matters. The votes will be counted, tabulated and certified by a representative of Broadridge Financial Solutions, who will serve as the inspector of elections at the Annual Meeting.

        Abstentions are included in the shares present at the Annual Meeting for purposes of determining whether a quorum is present, and are counted as a vote against for purposes of determining whether a proposal is approved. Broker non-votes (when shares are represented at the Annual Meeting by a proxy specifically conferring only limited authority to vote on certain matters and no authority to vote on other matters) are included in the determination of the number of shares represented at the Annual Meeting for purposes of determining whether a quorum is present but are not counted for purposes of determining whether a proposal has been approved and thus have no effect on the outcome.

Voting Your Shares

        If you are the record holder of your shares, you may vote in one of four ways. You may vote by submitting your proxy over the Internet, by telephone, or by mail or you may vote in person at the Annual Meeting.

        You may vote over the Internet.    If you have Internet access, you may vote your shares from any location in the world by following the "Vote by Internet" instructions set forth on the enclosed proxy card.

        You may vote by telephone.    You may vote your shares by following the "Vote by Phone" instructions set forth on the enclosed proxy card.

        You may vote by mail.    You may vote by completing, dating and signing the proxy card that accompanies this proxy statement and promptly mailing it in the enclosed postage-prepaid envelope. You do not need to put a stamp on the enclosed envelope if you mail it in the United States. The shares you own will be voted according to the instructions on the proxy card you mail. If you return the proxy card, but do not give any instructions on a particular matter described in this proxy statement, the shares you own will be voted in accordance with the recommendations of our board of directors. Our board of directors recommends that you vote FOR Proposals 1 and 2.

        You may vote in person.    If you attend the Annual Meeting, you may vote by delivering your completed proxy card in person or you may vote by completing a ballot. Ballots will be available at the meeting.

Changing Your Vote; Revocation of Proxy

        Voting over the Internet or by telephone or execution of a proxy will not in any way affect a stockholder's right to attend the Annual Meeting and vote in person. A proxy may be revoked before it is used to cast a vote. To revoke a proxy, a stockholder must:

•

file with our corporate secretary, at or before the taking of the vote, a written notice of revocation bearing a later date than the proxy;



•

duly execute a later dated proxy relating to the same shares and deliver it to our corporate secretary before the taking of the vote; or



•

attend the Annual Meeting and vote in person. Attendance at the Annual Meeting, if a stockholder does not vote, will not be sufficient to revoke a proxy.

        Any written notice of revocation or subsequent proxy should be sent to us at the following address: Momenta Pharmaceuticals, Inc., 675 West Kendall Street, Cambridge, MA 02142, Attention: Steven N. Avruch, Esq., Corporate Secretary. The shares represented by all properly executed proxies received in time for the Annual Meeting will be voted as specified in those proxies. If the shares you own are held in your name and you do not specify in the proxy card how your shares are to be voted, they will be voted in favor of the election of the directors named in this proxy statement, in favor of the ratification of the appointment of Ernst & Young LLP as our independent registered public accounting firm and, in the discretion of the persons appointed as proxies, on any other items that may properly come before the Annual Meeting. If the shares you own are held in "street name," the bank or brokerage firm, as the record holder of your shares, is required to vote your shares in accordance with your instructions. To vote your shares held in "street name," you will need to follow the directions provided to you by your bank or brokerage firm.

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PROPOSAL ONE

ELECTION OF DIRECTORS

Board Recommendation

        The board of directors recommends a vote "FOR" the election of each of Mr. Crane, Mr. Hutt and Ms. Fanucci as Class I directors.

        We have three classes of directors, currently consisting of three Class I directors, four Class II directors and four Class III directors. At each annual meeting, directors are elected for a full term of three years to succeed those whose terms are expiring. The terms of the three classes are staggered in a manner so that only one class is elected by stockholders annually. Alan L. Crane, Peter Barton Hutt and Marsha H. Fanucci are currently serving as Class I directors. The Class I directors elected this year will serve as members of our board of directors until the 2011 annual meeting of stockholders, or until their respective successors are elected and qualified.

        The persons named in the enclosed proxy card will vote to elect Mr. Crane, Mr. Hutt and Ms. Fanucci as Class I directors unless you withhold authority to vote for the election of any or all nominees by marking the proxy card (whether executed by you or through the Internet or telephonic voting). Mr. Crane, Mr. Hutt and Ms. Fanucci currently serve on our board of directors. The nominees have indicated their willingness to continue to serve if elected. However, if any director nominee should be unable to serve, the shares of common stock represented by proxies may be voted for a substitute nominee designated by our board of directors. Our board of directors has no reason to believe that the nominees will be unable to serve if elected.

        On April 10, 2008, Stephen T. Reeders, a Class II director and a member of audit committee, submitted his resignation effective as of the date of the Annual Meeting. Our board of directors has provided that our full board of directors shall be comprised of eleven members. We are actively recruiting potential candidates to fill this directorship. This vacancy, when it occurs, may be filled by a vote of a majority of the directors then in office. The director elected to fill this vacancy shall hold office until the next election of the class for which such director shall have been chosen.

        No director or executive officer is related by blood, marriage or adoption to any other director or executive officer. No arrangements or understandings exist between any director or person nominated for election as a director and any other person pursuant to which such person is to be selected as a director or nominee for election as a director.

3

Our Board of Directors

        Set forth below for each of our directors, including the Class I director nominees, is information as of April 15, 2008 with respect to each director's (a) name and age, (b) positions and offices with us, (c) principal occupation and business experience during at least the past five years, (d) directorships, if any, of other publicly-held companies and (e) the year such person became a member of our board of directors.

4

5

6

7

(1)

Member of Audit Committee.

(2)

Member of Compensation Committee.

(3)

Member of Nominating and Corporate Governance Committee.

(4)

Member of Science Committee.

        For information relating to shares of our common stock owned by and options granted to each of our directors, see the disclosure set forth under the headings "Executive Compensation—Compensation of Directors" and "Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters."

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CORPORATE GOVERNANCE

General

        We believe that good corporate governance is important to ensure that Momenta is managed for the long-term benefit of our stockholders. During the past year, we have continued to review our corporate governance policies and practices and to compare them to those suggested by various authorities in corporate governance and the practices of other public companies. We have also continued to review the provisions of the Sarbanes-Oxley Act of 2002, the new and proposed rules of the Securities and Exchange Commission and the listing standards of the NASDAQ Global Market.

        This section describes key corporate governance practices that we have adopted. Complete copies of our corporate governance guidelines, committee charters and code of conduct described below are available on the "Corporate Governance" section of our website at www.momentapharma.com. Alternatively, you may request a copy of any of these documents by writing to Momenta Pharmaceuticals, Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142, attention: Richard P. Shea, Chief Financial Officer and Treasurer, telephone: (617) 491-9700.

Corporate Governance Guidelines

        Our board of directors has adopted corporate governance guidelines to assist our board of directors in the exercise of its duties and responsibilities and to serve the best interests of Momenta and its stockholders. These guidelines, which provide a framework for the conduct of the board of directors' business, provide that:

•

the principal responsibility of the directors is to oversee the management of Momenta;



•

a majority of the members of the board of directors shall be independent directors;



•

the independent directors meet periodically in executive session;



•

directors shall have full and free access to management and, as necessary and appropriate, independent advisors;



•

new directors shall participate in an orientation program and all directors are expected to participate in continuing director education on an ongoing basis; and



•

at least annually the board of directors and its committees will conduct a self-evaluation to determine whether they are functioning effectively.

Board Determination of Independence

        Under applicable NASDAQ rules, a director will only qualify as an "independent director" if, in the opinion of our board of directors, that person does not have a relationship which would interfere with the exercise of independent judgment in carrying out the responsibilities of a director. Our board of directors has determined that none of Peter Barrett, John K. Clarke, Marsha H. Fanucci, Peter Barton Hutt, Stephen T. Reeders, Bennett M. Shapiro or Elizabeth Stoner, who currently comprise our audit, compensation and nominating and corporate governance committees, has a relationship that would interfere with the exercise of independent judgment in carrying out the responsibilities of a director and that each of these directors is "independent" as that term is defined under Rule 4200(a)(15) of the NASDAQ Marketplace Rules. Our board reached a similar determination with respect to Paul Goldenheim, who served as a director from May 2006 until May 2007.

        In determining the independence of the directors listed above, our board of directors considered each of the transactions discussed in "Certain Relationships and Related Transactions."

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Board Meetings and Attendance

        Our board of directors met 13 times during the fiscal year ended December 31, 2007, or Fiscal 2007, either in person or by teleconference. During Fiscal 2007, each director, with the exception of Peter Barton Hutt, Robert S. Langer, Jr., Stephen T. Reeders and Elizabeth Stoner attended at least 75% of the aggregate of the total number of board meetings and the total number of meetings held by all committees on which he or she then served. Mr. Hutt attended 75% of the regularly scheduled quarterly meetings of the board of directors and attended 67% of the special meetings of the board of directors. Dr. Langer attended 75% of the regularly scheduled quarterly meetings of the board of directors and attended 56% of the special meetings of the board of directors. Dr. Reeders attended 100% of the regularly scheduled quarterly meetings of the board of directors and attended 67% of the special meetings of the board of directors. Dr. Stoner joined the board of directors in October 2007 and was able to attend only one of the two board meetings held after her election.

Director Attendance at Annual Meetings of Stockholders

        Our corporate governance guidelines provide that directors are responsible for attending the annual meeting of stockholders. With the exception of Dr. Langer, all of our directors attended the 2007 annual meeting of stockholders.

Board Committees

        Our board of directors has established four standing committees—audit, compensation, nominating and corporate governance and science—each of which operates under a charter that has been approved by our board of directors. Current copies of the audit, compensation and nominating and corporate governance committee charters are posted on the Corporate Governance section of our website located at www.momentapharma.com.

        Our board of directors has determined that all of the members of each of the board of directors' standing committees (except the science committee) are independent as defined under the rules of the NASDAQ Stock Market, Inc. including, in the case of all members of the audit committee, the independence requirements contemplated by Rule 10A-3 under the Securities Exchange Act of 1934, as amended, or the Exchange Act.

Audit Committee

        The audit committee currently consists of Marsha H. Fanucci, John K. Clarke and Stephen T. Reeders. Ms. Fanucci chairs the audit committee. The audit committee was reconstituted in March 2004 and currently acts under a charter that was adopted and approved effective in June 2004 and that was amended and restated in each of December 2006 and March 2007. The audit committee held nine meetings in Fiscal 2007. It is anticipated that Ms. Fanucci, if elected to the board of directors by our stockholders, and Mr. Clarke will continue to serve on the audit committee. We are actively recruiting potential candidates to serve on the committee upon Mr. Reeders's departure. Our audit committee's responsibilities include:

•

appointing, approving the compensation of, and assessing the independence of our independent registered public accounting firm;



•

overseeing the work of our independent registered public accounting firm, including through the receipt and consideration of certain reports from such firm;



•

reviewing and discussing with management our annual and quarterly financial statements and related disclosures;



•

monitoring our internal control over financial reporting and disclosure controls and procedures;

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•

discussing our risk management policies;



•

establishing policies regarding hiring employees from the independent registered public accounting firm and procedures for the receipt and retention of accounting related complaints and concerns;



•

meeting independently with our independent registered public accounting firm and management;



•

reviewing and approving or ratifying any related person transactions; and



•

preparing the audit committee report required by Securities and Exchange Commission rules (which is included on page 62 of this proxy statement).

        Our board of directors has determined that each of Marsha H. Fanucci and John K. Clarke is an "audit committee financial expert" as defined by applicable Securities and Exchange Commission rules.

Compensation Committee

        The compensation committee currently consists of Peter Barrett, Peter Barton Hutt, Bennett M. Shapiro and Elizabeth Stoner. Mr. Barrett chairs the compensation committee. The compensation committee was reconstituted in March 2004 and currently acts under a charter that was adopted and approved effective in June 2004 and that was amended restated in March 2007. The compensation committee held 12 meetings in Fiscal 2007. It is anticipated that Mr. Hutt, if elected to the board of directors by our stockholders, and Drs. Barrett, Shapiro and Stoner will continue to serve on the compensation committee. Our compensation committee's responsibilities include:

•

annually reviewing and approving corporate goals and objectives relevant to compensation of our chief executive officer, or CEO;



•

determining the CEO's compensation;



•

reviewing and approving, or making recommendations to the board of directors with respect to, the compensation of our other executive officers;



•

overseeing an evaluation of our senior executives;



•

overseeing and administering our equity incentive plans;



•

reviewing and making recommendations to the board of directors with respect to director compensation;



•

reviewing and discussing annually with management our "Compensation Discussion and Analysis," which is included beginning on page 18 of this proxy statement; and



•

preparing the compensation committee report required by Securities and Exchange Commission rules, which is included on page 50 of this proxy statement.

        The processes and procedures followed by our compensation committee in considering and determining executive and director compensation are described below under the heading "Executive and Director Compensation Processes."

Nominating and Corporate Governance Committee

        Our nominating and corporate governance committee currently consists of Peter Barton Hutt, Peter Barrett and Bennett M. Shapiro. Mr. Hutt chairs the nominating and corporate governance committee. The nominating and corporate governance committee was established in March 2004 and currently acts under a charter that was adopted and approved effective in June 2004 and that was amended in September 2006. The nominating and corporate governance committee held eight meetings in Fiscal 2007. It is anticipated that Mr. Hutt, if elected to the board of directors by our stockholders,

11

and Drs. Barrett and Shapiro will continue to serve on the nominating and corporate governance committee. Our nominating and corporate governance committee's responsibilities include:

•

identifying individuals qualified to become board members;



•

recommending to the board of directors the persons to be nominated for election as directors and to each of the board's committees;



•

reviewing and making recommendations to the board of directors with respect to management succession planning;



•

reviewing and assessing our code of business conduct and ethics;



•

developing and recommending to the board of directors corporate governance principles; and



•

overseeing an annual evaluation of the board of directors.

        The processes and procedures followed by our nominating and corporate governance committee in identifying and evaluating director candidates are described below under the heading "Director Nomination Process."

Science Committee

        Our science committee currently consists of Bennett M. Shapiro, Robert S. Langer, Jr., Ram Sasisekharan and Elizabeth Stoner. Dr. Shapiro chairs the science committee. The science committee was established in March 2007 and currently acts under a charter that was adopted and approved effective in April 2007. The science committee held five meetings in Fiscal 2007. Our science committee's responsibilities include:

•

reviewing the scientific, clinical, regulatory and intellectual property strategies that underlie our major research and development programs;



•

reviewing the annual research and development budget and allocation of resources to certain of our programs;



•

reviewing the organization and structure of the research and development organization; and



•

assessing the attainment of research and development milestones.

Executive and Director Compensation Processes

        Our compensation committee has implemented an annual performance review program for our executives focused around annual corporate goals that are proposed by management, reviewed by the compensation committee and approved by the board of directors. These corporate goals target the achievement of specified operational and financial goals; specific research, clinical, regulatory, commercial or compliance milestones; and business development and financing initiatives. Individual performance is evaluated in part by reviewing the extent to which such performance facilitates the achievement of our annual corporate and business goals. Annual salary increases, individual components of annual incentive cash bonus awards and equity awards for each of our Named Executives are tied to a combination of achievement of corporate goals and individual performance.

        During the first calendar quarter of each year, we evaluate individual performance as well as corporate performance against the corporate goals for the recently completed year. Each executive's evaluation begins with a written self-assessment, which is submitted to the CEO. The CEO then prepares a written evaluation based on the executive's self-assessment, the CEO's own evaluation and input from others within Momenta. This process leads to a recommendation by the CEO and our Vice President, Human Resources with respect to salary increases, annual incentive cash bonus awards and equity awards for each of our Named Executives, which is then reviewed and approved by the

12

compensation committee. In the case of the CEO, his individual performance evaluation is conducted by the compensation committee, utilizing input from the board of directors and from selected executive officers in connection with an annual 360-performance review, which determines his compensation changes and awards. For all executives, annual base salary increases, annual incentive cash bonus awards and annual stock option grants and restricted stock awards, to the extent granted, are implemented during the first calendar quarter of the year.

        The compensation committee has delegated to Craig A. Wheeler, our CEO, the authority to make stock option grants under our 2004 Stock Incentive Plan, as amended, to newly-hired employees below the senior director level based on a number of options within a range as set forth in a matrix previously approved by the board of directors. Grants to newly-hired employees, whether made either by the CEO or by the compensation committee, are made on regularly scheduled monthly dates that occur outside of regularly scheduled quarterly financial blackout periods.

        The compensation committee has the authority to retain compensation consultants and other outside advisors to assist in the evaluation of executive officer compensation. To assist the compensation committee in discharging its responsibilities, in March 2007 the compensation committee retained an independent compensation consultant, Radford Surveys & Consulting, a business unit of AON Corporation, which we refer to as Radford, to evaluate certain aspects of our compensation practices and to assist in developing and implementing our incentive compensation program. Radford provided research regarding best practices, advice on the appropriate strategic use of reward vehicles, performed analyses of competitive compensation levels, assisted in our promotion process and advised on the use of restricted stock for key talent. With this information, our management developed recommendations for Fiscal 2007 that were reviewed and approved by the compensation committee in connection with formulating and approving compensation awards.

Director Nomination Process

        The process followed by our nominating and corporate governance committee to identify and evaluate director candidates includes requests to board members and others for recommendations, meetings from time to time to evaluate biographical information and background material relating to potential candidates and interviews of selected candidates by members of the nominating and corporate governance committee and other members of the board of directors, as applicable. In addition, during Fiscal 2007, the nominating and corporate governance committee used the services of an executive search firm to help identify and evaluate potential director candidates.

        In considering whether to recommend any particular candidate for inclusion in the board's slate of recommended director nominees, the nominating and corporate governance committee applies the criteria attached to its charter. These criteria include the candidate's integrity, business acumen, knowledge of our business and industry, experience, diligence, conflicts of interest and the ability to act in the interests of all stockholders. The nominating committee does not assign specific weights to particular criteria and no particular criterion is a prerequisite for each prospective nominee. We believe that the backgrounds and qualifications of our directors, considered as a group, should provide a composite mix of experience, knowledge and abilities that will allow the board of directors to fulfill its responsibilities.

        Stockholders may recommend individuals to the nominating and corporate governance committee for consideration as potential director candidates by submitting their names, together with appropriate biographical information and background materials and a statement as to whether the stockholder or group of stockholders making the recommendation has beneficially owned more than 5% of our common stock for at least a year as of the date such recommendation is made, to the nominating and corporate governance committee, c/o Steven N. Avruch, Esq., Corporate Secretary, Momenta Pharmaceuticals, Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142. Assuming that

13

appropriate biographical and background material has been provided on a timely basis, the nominating and corporate governance committee will evaluate stockholder-recommended candidates by following substantially the same process, and applying substantially the same criteria, as it follows for candidates submitted by others.

        Stockholders also have the right under our bylaws to directly nominate director candidates, without any action or recommendation on the part of the nominating and corporate governance committee or the board of directors, by following the procedures set forth under Section 1.10, "Nomination of Directors," in our amended and restated bylaws that are described under the heading "Stockholder Proposals."

        In October 2007, Elizabeth Stoner was appointed by our board of directors as a new director. Dr. Stoner was originally proposed to the nominating and corporate governance committee by a member of our board of directors.

Communicating with the Independent Directors

        Our board of directors will give appropriate attention to written communications that are submitted by stockholders, and will respond if and as appropriate. The chairman of the board of directors (if an independent director), or the lead director (if one is appointed), or otherwise the chairperson of the nominating and corporate governance committee, subject to advice and assistance from the CEO and, if requested, outside legal counsel, is primarily responsible for monitoring communications from stockholders and for providing copies of summaries of such communications to the other directors as he or she considers appropriate.

        Under procedures approved by a majority of the independent directors, communications are forwarded to all directors if they relate to important substantive matters and include suggestions or comments that the chairman of the board considers to be important for the directors to know. In general, communications relating to corporate governance and corporate strategy are more likely to be forwarded than communications relating to ordinary business affairs, personal grievances and matters as to which we tend to receive repetitive or duplicative communications.

        Stockholders who wish to send communications on any topic to the board of directors should address such communications to board of directors c/o Steven N. Avruch, Esq., Corporate Secretary, Momenta Pharmaceuticals, Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142.

Code of Business Conduct and Ethics

        We have adopted a written code of business conduct and ethics that applies to our directors, officers and employees, including our principal executive officer, principal financial officer, principal accounting officer or controller, or persons performing similar functions. We have posted a current copy of the code on our website, which is located at www.momentapharma.com. In addition, we intend to post on our website all disclosures that are required by law or NASDAQ Global Market listing standards concerning any amendments to, or waivers from, any provision of the code.

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Section 16(a) Beneficial Ownership Reporting Compliance

        Section 16(a) of the Exchange Act requires our directors, executive officers and the holders of more than 10% of our common stock to file with the Securities and Exchange Commission initial reports of ownership of our common stock and other equity securities on a Form 3 and reports of changes in such ownership on a Form 4 or Form 5. Officers, directors and 10% stockholders are required by Securities and Exchange Commission regulations to furnish us with copies of all Section 16(a) forms they file. Based solely on our review of copies of Section 16(a) reports furnished to us and representations made to us, we believe that, except as set forth below, during Fiscal 2007 our officers, directors and holders of more than 10% of our common stock complied with all Section 16(a) filing requirements:

•

a late Form 4 report was filed for Ganesh Venkataraman on May 25, 2007 to report the grant of an option to purchase 15,000 shares of our common stock on February 22, 2007;



•

a late Form 4 report was filed for Steven B. Brugger on May 25, 2007 to report the grant of an option to purchase 22,500 shares of our common stock on February 22, 2007;



•

a late Form 4 report was filed for Richard P. Shea on May 25, 2007 to report the grant of an option to purchase 7,000 shares of our common stock on February 22, 2007;



•

a late Form 4 report was filed for John E. Bishop on March 22, 2007 to report the grant of an option to purchase 37,500 shares of our common stock on February 22, 2007;



•

a late Form 4 report was filed for Stephen T. Reeders on March 28, 2007 to report the sale of 242,466 shares of our common stock and the distribution of 430,000 shares by MVM International Life Sciences Fund No. 1 L.P. of our common stock on January 10, 2007;



•

a late Form 4 report was filed for Richard P. Shea on December 20, 2007 to report the grant of an option to purchase 15,000 shares of our common stock and an award of 15,000 shares of restricted common stock on August 15, 2007; and



•

a late Form 5 report was filed for John K. Clarke on April 22, 2008 to report the gift of 4,400 shares of our common stock on December 15, 2005 and the acquisition of 2,026 shares of our common stock on November 20, 2006.

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Our Executive Officers

        The following table sets forth the names, ages and positions of our current executive officers as of April 15, 2008:

(1)

Richard P. Shea has been our Senior Vice President and Chief Financial Officer since July 2007. From October 2003 until July 2007 he served as Vice President and Chief Financial Officer. From April 2002 to April 2003, Mr. Shea served as Chief Operating Officer for Variagenics, Inc., a pharmacogenomics company. From March 2000 to April 2002, Mr. Shea served as Variagenics' Chief Financial Officer and from February 1999 to March 2000, he served as Vice President, Finance and Administration. While at Variagenics, Mr. Shea was responsible for finance, legal, investor relations, human resources and operations. Mr. Shea is a CPA and received his A.B. from Princeton University and his M.B.A. from Boston University.

(2)

Ganesh Venkataraman, Ph.D. is a co-founder of our company and has been our Chief Scientific Officer since September 2007 and our Senior Vice President, Research since April 2005. From January 2002 until April 2005 he served as Vice President, Technology. From August 2000 to January 2003, Dr. Venkataraman served as the Director of Bioinformatics for the Consortium for Functional Glycomics, a multi-million dollar NIH initiative to study the role of complex sugars in biology. From March 1995 to July 2000, Dr. Venkataraman was a research faculty member at the Harvard M.I.T. division of Health and Sciences and Technology, where he investigated the biochemistry and biophysics of carbohydrates and research in the area of analytical techniques for complex carbohydrates. Dr. Venkataraman received his M.S. and Ph.D. in Chemical Engineering from the Massachusetts Institute of Technology.

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(3)

Steven B. Brugger has been our Chief Operating Officer since September 2007. He served as Senior Vice President, Strategic Business Operations from April 2005 until September 2007 and as Vice President, Strategic Product Development from August 2002 to April 2005. From 2000 to August 2002, Mr. Brugger served as a Vice President for Millennium Pharmaceuticals, Inc., a biopharmaceutical company, and from October 1999 through 2000 he served as a Senior Director. While at Millennium, Mr. Brugger built Millennium's strategic marketing, project management and portfolio management capabilities. During his tenure at Millennium, Mr. Brugger served as Head of Commercial Development, General Manager of the Inflammation and Metabolic Business Units, and Development Projects Leader for the Aventis and Abbott collaborations. Prior to joining Millennium, Mr. Brugger worked for 19 years in the pharmaceutical industry, with his most recent position being as an Executive Director, Marketing at Novartis Pharmaceuticals. Mr. Brugger received his B.A. in Biology from Susquehanna University and his M.B.A. from Rutgers University.

(4)

John E. Bishop, Ph.D. has been Senior Vice President, Pharmaceutical Sciences since December 2006. He served as Vice President, Pharmaceutical Sciences and Manufacturing from November 2004 to December 2006. From August 2000 to October 2004, Dr. Bishop served as Director and Head of Process Development (Chemical and Biologics) at Millennium Pharmaceuticals, Inc. During that period, he also led the Chemistry, Manufacturing and Controls (CMC) team for Velcade®. From July 1994 to August 2000, Dr. Bishop was a Process R&D leader at the DuPont Merck Pharmaceutical Company, with responsibility for the division's process development, technology transfer, and vendor management activities. Dr. Bishop received his B.S. magna cum laude in Chemistry and German from Tufts University, his Ph.D. in Organic Chemistry from UC Berkeley and his M.B.A. from Northeastern University.

(5)

James M. Roach, M.D. has been Senior Vice President, Development and Chief Medical Officer since February 2008. From January 2006 to February 2008, Dr. Roach served as Senior Vice President, Medical Affairs at Sepracor Inc., where he also served as Vice President, Medical Affairs from July 2002 to December 2005 and as Executive Medical Director, Medical Affairs from January 2002 to June 2002. Dr. Roach has also held senior clinical research and/or medical affairs positions at Millennium Pharmaceuticals, Inc., LeukoSite, Inc., Medical and Technical Research Associates, Inc. and Astra USA, where he began his career in the industry in September 1995. Dr. Roach is board certified in Internal Medicine, Pulmonary Disease, and Critical Care Medicine and is an Assistant Clinical Professor of Medicine at Harvard Medical School and an Associate Physician at Brigham and Women's Hospital. Dr. Roach received his B.A. in biology and philosophy from the College of the Holy Cross and his M.D. from Georgetown University School of Medicine. He completed his residency in Internal Medicine and fellowship in Pulmonary and Critical Care Medicine at the Walter Reed Army Medical Center in Washington, D.C.

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EXECUTIVE COMPENSATION

Compensation Discussion and Analysis

Executive Summary

        During Fiscal 2007, Momenta achieved significant accomplishments, but also faced a number of business and regulatory challenges. The accomplishments included: consummating the acquisition of Parivid LLC; negotiating and finalizing our second collaboration with Sandoz; and advancing our M118 and M356 programs. The challenges included: reacting, and preparing to respond, to the FDA's request for additional data to address the potential for immunogenicity of our M-Enoxaparin candidate; subleasing our 300 Third Street facility amid cash conservation pressures; and the need to continue to upgrade our infrastructure in many areas. Details of many of these challenges can be found in our Form 10-K, Form 10-Q and Form 8-K filings.

        In response to these challenges, we believed that there was a critical need to build employee morale as well as to build trust with our public stockholders. Our board of directors determined that we needed to take steps to continue to transform Momenta into a high-performing company that could provide value to stockholders over the long term. As part of this process, our board of directors made changes in our senior leadership. In July 2007, Richard P. Shea, who had been our Vice President and Chief Financial Officer, was promoted to Senior Vice President and Chief Financial Officer. In September 2007, we announced that Steven Brugger had been appointed as Chief Operating Officer; Mr. Brugger had served as our Senior Vice President, Strategic Product Development from August 2002 to April 2005. Also in September 2007, Ganesh Venkataraman, our Senior Vice President, Research, was promoted to the position of Chief Scientific Officer and Senior Vice President, Research.

        We also made significant changes in our policies and procedures in the area of executive compensation, including redesigning our compensation program, adopting stock ownership guidelines and recommending entering into employment agreements with members of our senior leadership team. See "Redesign of the Compensation Program in 2007," "Stock Ownership Guidelines" and "—Executive Employment Agreements with Richard P. Shea, Ganesh Venkataraman, Steven B. Brugger and John E. Bishop" below for details. These changes were prompted in large measure by an independent review of our historic compensation practices conducted by our compensation committee and Radford Surveys & Consulting, a business unit of AON Corporation, which we refer to as Radford.

Redesign of the Compensation Program in 2007

        In 2007, our compensation committee determined that the executive compensation program should be redesigned to:

•

link pay to performance (measured on the corporate as well as individual level);



•

reinforce business strategy and reflect and reinforce Momenta's values;



•

reward teamwork and integrity;



•

motivate our people to achieve meaningful results in support of our company goals;



•

keep things simple to promote understanding and enable employees to make informed decisions; and



•

retain our management team and other employees.

        The objectives of our redesigned executive compensation program are to align the interests of management with the interests of stockholders through a system that correlates compensation to enterprise objectives and, to a lesser extent, individual performance. Our program is geared for short and long-term performance, with the goal of increasing stockholder value over the long term. We also

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emphasize retention in our program. The life sciences industry is science-focused and driven by innovation, and as a result, Momenta believes that executives with industry knowledge are more likely to excel, but this limits the recruiting pool and makes retention a higher priority than might be the case in industry generally.

        Our executive compensation philosophy is based on the following principles:

•

Competitive and Fair Compensation.  We believe that the performance of our Named Executives should be viewed, and their overall compensation should be determined, in the context of our industry, the competitive landscape and our performance. While we do not have an exact formula for allocating between cash and non-cash compensation, we try to balance short-term cash compensation and long-term equity by offering reasonable base salaries, market-competitive benefits, annual incentive cash bonuses and opportunities for financial growth through our stock option and other equity incentive programs. These components are established separately and viewed distinctly by our compensation committee. For example, a given level of cash compensation does not reduce or offset awards of equity compensation.



•

Sustained Performance.  In determining total compensation, we stress a philosophy that is performance driven. Our Named Executives are primarily rewarded based upon an assessment of corporate performance and secondarily on individual performance. Corporate performance is evaluated by reviewing the extent to which established corporate goals are met. Individual performance is evaluated by reviewing how each Named Executive contributed in the context of overall corporate goals. Our compensation philosophy emphasizing performance permeates total compensation for both executives and non-executives. We believe that the design of our executive compensation program affects all of our employees and, because the performance of every employee is important to our success, we are cognizant of the effect that executive compensation may have on each member of our team.

        In redesigning and formalizing our compensation program, in February 2007, Radford and our compensation committee focused predominantly on two areas of compensation: our annual incentive cash bonus program and our equity award program. With respect to our bonus program, Radford gathered competitive data from the Radford Biotechnology Executive Survey, focusing on companies with 150 to 499 employees. Specifically, Radford evaluated the prevalence of formalized bonus plans, the cost of such programs as a percentage of payroll, the incidence of minimum/maximum levels of performance and associated payout, the number of issuers that employed metric weighting between company and individual performance and the timing and performance period for short-term incentive awards. Whereas our historical cash bonus program was primarily linked to individual performance, the survey data showed that most short-term incentive programs weighted corporate performance as approximately 60% of the bonus opportunity, 98% of these programs used a percentage of salary as the basis for determining target bonuses and almost all companies paid bonuses annually with awards paid for the prior twelve months of performance. With that data as a backdrop, our 2007 annual cash incentive program was designed to reward our CEO solely on corporate performance based on metrics defined by management and approved by our board of directors and, with respect to executives below the CEO level, 75% in relation to corporate performance and 25% based on individual contribution toward those corporate goals.

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        With respect to our equity award program, Radford reviewed information from the 2006 Radford Biotechnology Stock by Level Equity Report and evaluated 21 peer companies to better understand aggregate equity use and executive long-term incentive awards. The specific "peer companies" evaluated included:

        A regression analysis was used to determine appropriate long-term incentive values by grade, drawing upon the average salary level for each grade, and competitive data were collected for Black-Scholes equity value and number of options. It was noted that due to our hiring needs, our 2006 equity burn rate exceeded the 75^th percentile; however, both issued and total stock overhang trailed the market 50^th percentile. Based on the data reviewed, Radford and our compensation committee determined that our forward-looking long-term incentive program must balance multiple considerations, including building a management team for the future, retaining key employees and anticipating future business outlook, while adhering to a target burn rate, program guidelines based on market competitive practices of broad life sciences companies and the appropriate mix of equity vehicles. We grant stock options to executives and other employees upon commencement of employment. The size of the initial stock option grant has been determined by reference to a pre-set range approved by our board of directors generally intended to reflect the level of the employee's position. We also make annual performance grants, and those grants have also been made pursuant to a pre-set range approved by our board of directors and have been intended to reflect the level of the employee's position with us as well as individual performance relative to his or her goals and generally represent approximately 10% of the employee's initial grant. On a going forward basis, it was determined that initial stock option grants would be reduced and that the range for annual performance grants would be expanded to allow for larger annual grants.

        Radford also reviewed the salary structure for our Named Executives and other employees. For our Named Executives, Radford based its review on a blend of market data and proxy data from a positional perspective. For non-executive positions, Radford differentiated between scientific and non-scientific positions based upon departmental assignments. Radford concluded that base salaries were generally in the 50^th percentile and it was determined that no change would be made in base salaries, although Radford recommended a review of market data to determine merit increases in salary later in 2007. In order to determine the appropriate target level for company-wide salary increases for 2008, we obtained survey data from the following sources: WorldatWork Budget Survey 07/08; Mercer 2007/2008 U.S. Compensation Planning; ERI Salary Increase Survey 2008; Compdata Survey (Merit Only); Hewitt Associates (est); and Radford Life Sciences. These surveys were utilized to assure that our proposed merit salary increases were market competitive. The projected merit salary increases for 2008 contained in five of the six surveys were between 3.8% and 4.0% of current base salaries of all exempt employees. The average projected merit salary increase for executives was slightly above 4.0%. Using this data, we set a target level of merit salary increase at 4.0%.

        We do not use "internal pay equity" as a constraint on compensation paid to our CEO or other Named Executives. Such systems typically put a ceiling on part or all of an executive's compensation based on a specified multiple of compensation awarded to another executive or a class of employees of Momenta. Our management and our compensation committee do not believe that such arbitrary limitations are an appropriate way to make compensation decisions for our executives. Instead, we rely

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on the judgment of the compensation committee, after considering recommendations from management and external advisors, available market data and evaluations of executive performance, in the context of a program that is weighted heavily in favor of performance-based compensation for our Named Executives.

Stock Ownership Guidelines

        In September 2007, our board of directors, upon recommendation of the compensation committee, approved a stock ownership and retention program for our executive officers and non-employee directors, or Covered Individuals. The purpose of the program is to ensure that each Covered Individual has a long-term equity stake in Momenta, to more closely align the interests of the Covered Individuals with those of our stockholders and to further promote our commitment to sound corporate governance.

        Under the program's guidelines, (i) our President and CEO is expected to hold shares of our common stock having an aggregate value equal to or greater than three times his or her annual base salary, (ii) other executive officers are expected to hold shares of our common stock having an aggregate value equal to or greater than one time their annual base salary and (iii) non-employee directors are expected to hold shares of our common stock having an aggregate value equal to or greater than three times their then current annual retainer for general board membership, excluding subcommittee retainers, per meeting or other similar fees.

        The Covered Individuals are expected to comply with these guidelines by the later of March 31, 2013 and the fifth anniversary that each such person becomes a Covered Individual. Until the applicable minimum share requirement is achieved, each Covered Individual is required to retain all shares of restricted stock upon the lapse of vesting restrictions, net of shares surrendered or sold to pay applicable withholding taxes. Once a Covered Individual has met these guidelines, he or she must continue to satisfy the guidelines so long as he or she remains a Covered Individual. Each Covered Individual's satisfaction of the minimum share requirement will be measured on an annual basis. Shares that count toward satisfaction of the guidelines include:

•

shares of common stock owned outright by the Covered Individual or his or her spouse or minor children;



•

shares of common stock held in trust for the benefit of the Covered Individual or his or her spouse or minor children; and



•

restricted stock or restricted stock units for which applicable restrictions have lapsed.

        The minimum share requirement may be waived, at the discretion of the compensation committee, if compliance would create severe hardship, would prevent a Covered Individual from complying with a court order, as in the case of a divorce settlement, or when a Covered Individual attains the age of 62.

Determining Executive Compensation (Roles and Process)

        Utilizing the philosophy outlined above, our compensation committee determines the parameters of the executive compensation program, including appropriate target levels and performance measures, and administers our executive compensation program. This section discusses, in greater detail, the roles and process underlying the application of our executive compensation philosophy.

Role of CEO in Compensation Decisions

        The CEO's role in the compensation process begins with the establishment of our corporate and business performance objectives against which the payment of annual incentive bonus awards will be measured. Our CEO, together with our executive team, discusses and formulates annual corporate and

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business goals. These goals are presented to our compensation committee who refines the goals and recommends them for approval by our board of directors. The CEO's role in the compensation process continues with his review of our Named Executives. Our CEO elicits 360-performance reviews with respect to each of our Named Executives. These 360-performance reviews are written evaluations of each Named Executive that are submitted to our CEO by our employees who interact with these Named Executives. The CEO then assimilates the feedback from these 360-performance reviews into formal written evaluations of each Named Executive, including the CEO's own evaluation of the Named Executive. The CEO's evaluation also included documenting each Named Executive's performance during the year, detailing accomplishments, areas of strength and areas for development pursuant. The CEO bases this evaluation on his knowledge of each Named Executive's performance and feedback provided by the 360-performance reviews. Each Named Executive is then rated based on their performance during the year. The CEO then sits down with each Named Executive and reviews their respective evaluations. The CEO then works directly with our Vice President, Human Resources to provide comprehensive recommendations for salary increases, individual components of annual incentive cash bonus awards and equity awards for each of our Named Executives. These recommendations are presented to, reviewed by and ultimately approved by our compensation committee.

        At the request of the compensation committee, our CEO attends all or portions of periodic meetings of the compensation committee, but does not attend portions of any meeting in which the compensation committee discusses his compensation or performance. In addition, our compensation committee reviews the recommendations from our CEO with respect to executive compensation trends among biotechnology companies, including the overall blend of salary, bonus and equity compensation within such group and his recommendations pertaining to our executive compensation program.

Role of the Compensation Committee

        Our compensation committee recognizes the importance of maintaining sound principles for the development and administration of our compensation program which is intended to strengthen the link between executive pay and performance. The compensation committee, in accordance with its written charter, oversees all aspects of our director, officer and other executive compensation policies. Based on the process described in "Role of CEO in Compensation Decisions," the CEO, together with our Vice President, Human Resources, makes a recommendation to the compensation committee on each Named Executive's compensation, except his own. Named Executives do not propose or seek approval for their own compensation. The compensation committee then determines the compensation of each of these Named Executives. The compensation committee also evaluates the CEO's performance and determines the CEO's compensation utilizing input from the board of directors and from selected executive officers in connection with an annual 360-performance review.

Role of External Advisors

        To assist the compensation committee in discharging its responsibilities, in February 2007, our compensation committee retained an independent compensation consultant, Radford, to evaluate certain aspects of our compensation practices and to assist in developing and implementing our incentive compensation program. Radford provided research regarding best practices, advice on the appropriate strategic use of reward vehicles, performed analyses of competitive compensation levels, assisted in our promotion process and advised on the use of restricted stock for key talent. As part of this process, members of the compensation committee reviewed materials provided and had the opportunity to meet independently with Radford at anytime throughout the year to discuss our executive compensation and to receive input and advice. Any written reports and studies provided by Radford are provided to the compensation committee. As compensation for services in 2007, we paid

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Radford a total of $96,530. Radford reported directly to the compensation committee and did not provide any other services to us other than those described in this section.

        We have not retained any other compensation consultant to review our policies and procedures relating to executive compensation. We expect that from time to time our compensation committee will engage one or more consultants to provide advice and resources.

Elements of Compensation

        Our compensation program is designed to reward each Named Executive based upon a combination of corporate and individual performance. Corporate performance is evaluated by reviewing the extent to which pre-set goals are met, which generally include the achievement of: specified operational and financial goals; specific research, clinical, regulatory, commercial or compliance milestones; and business development and financing initiatives. We evaluate individual performance in part by reviewing the extent to which individual performance facilitated the achievement of the corporate and business goals discussed above.

        The compensation package offered to each Named Executive is comprised of a combination of:

•

base salary;



•

annual incentive cash bonus awards;



•

annual equity awards;



•

other benefits, such as health, dental, disability and life insurance; and



•

severance and change-of-control payments.

        We maintain broad-based benefits that are provided to eligible employees, including health, dental, life and disability insurance and a 401(k) plan. Our Named Executives are eligible to participate in all of our employee benefit plans, in each case on the same basis as other employees.

        Base Salary.    Base salaries are established for our Named Executives at levels that are intended to reflect the scope of each Named Executive's industry experience, knowledge and qualifications, salary levels in effect for comparable positions within peer companies within our industry and internal comparability considerations. We believe that base salaries are a fundamental element of our executive compensation program. Base salaries are reviewed at least annually by our compensation committee, and are adjusted from time to time to ensure that our executive compensation structure remains aligned with our compensation objectives and are based upon various subjective criteria and the compensation paid by peer-group companies. Subjective performance criteria include an executive's ability to lead through motivating and inspiring others, to demonstrate the skills necessary to perform effectively in his or her area of responsibility, to recognize and pursue new business opportunities and to initiate programs to enhance our growth and success.

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        During early 2007, the compensation co