EXHIBIT 3.1 RESTATED CERTIFICATE OF INCORPORATION


                          CERTIFICATE OF INCORPORATION
                                       OF
                              REPLIGEN CORPORATION

                Incorporated pursuant to an original Certificate
               of Incorporation filed with the Secretary of State
                                  May 29, 1981

                      We, the undersigned, for the purpose of restating the
     Certificate of Incorporation of Repligen Corporation (hereinafter referred
     to as the "corporation" or the "Company") under the laws of the State of
     Delaware, hereby certify as follows:

         FIRST. The name of the corporation is Repligen Corporation.

         SECOND. The address of the registered office of the corporation in the
State of Delaware is 32 Loockerman Square, Suite L-100, Dover, Kent County,
Delaware, 19901. The name of the registered agent of the corporation at such
address is The Prentice-Hall Corporation System, Inc.

         THIRD. The purpose of the corporation is to engage in any lawful act or
activity for which corporations may be organized under the General Corporation
Law of Delaware, and specifically, without limiting the generality of the
foregoing, to engage in research, development, manufacture and marketing of
products produced in part by application of genetic engineering techniques.

         FOURTH. The total number of shares of stock which the Company shall
have authority to issue is thirty-five million (35,000,000), of which thirty
million (30,000,000) shares shall constitute Common Stock ("Common Stock"), each
such share having a par value of one cent, and five million (5,000,000) shares
shall constitute Preferred Stock ("Preferred Stock"), each such share having a
par value of one cent.

         The powers, preferences and rights of the Common Stock and the
Preferred Stock shall be as set forth below:

                                 PREFERRED STOCK

         1. DESIGNATION OF SERIES BY BOARD OF DIRECTORS. The shares of Preferred
Stock may be divided by the Board of Directors into and issued in one or more
series, and each series shall be designated so as to distinguish the shares
thereof from the shares of all other series. All shares of Preferred Stock shall
be identical with all other shares of Preferred Stock, except in respect of
particulars which may be fixed by the Board of Directors as hereinafter provided
pursuant to the authority which is hereby expressly vested in the Board of
Directors. Each share of a series shall be identical in all respects with all
other shares of such series, except as to the date from which dividends thereon
(if any) shall be cumulative on any series as to which dividends are cumulative.

         2. TERMS THAT MAY BE SET BY BOARD OF DIRECTORS. Before any shares of
Preferred Stock of any series shall be issued, the Board of Directors, pursuant
to authority hereby expressly vested in it, shall fix by resolution or
resolutions the following provisions in respect of the shares for each such
series provided that such provisions are not inconsistent with the provisions of
this Article FOURTH applicable to shares of all series of Preferred Stock then
outstanding:

            (a) The distinctive designations of each such series and the number
         of shares which shall constitute such series, if any, which number may
         be increased (except where otherwise provided by the Board of Directors
         in creating such series) or decreased (but not below the number of
         shares thereof then outstanding) from time to time by like action of
         the Board of Directors;


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            (b) The annual rate or amount of dividends payable on shares of such
         series, if any, whether such dividends shall be cumulative or
         non-cumulative, the conditions upon which and/or the dates when such
         dividends shall be payable and the date from which dividends on
         cumulative series shall accrue and be cumulative on all shares of such
         series issued prior to the payment date for the first dividend of such
         series;

            (c) Whether such series shall be redeemable or callable and, if so,
         the terms and conditions of such redemption or call, including the time
         or times when and the price or prices at which shares of such series
         shall be redeemed or called, and including the terms and conditions of
         any retirement or sinking fund for the purchase or redemption of shares
         of such series;

            (d) The amount payable on shares of such series in the event of
         liquidation, dissolution or winding up of the affairs of the Company;

            (e) Whether such series shall be convertible into or exchangeable
         for shares of any other class, or any series of the same or any other
         class and, if so, the terms and conditions thereof, including the date
         or dates when such shares shall be convertible into or exchangeable for
         shares of any other class, or any series of the same or any other
         class, the price or prices or the rate or rates at which shares of such
         series shall be so convertible or exchangeable, and any adjustments
         which shall be made, and the circumstances in which any such
         adjustments shall be made, in such conversion or exchange prices or
         rates;

            (f) Whether such series shall have any voting rights in addition to
         those prescribed by law and, if so, the terms and conditions of
         exercise of such voting rights;

            (g) The conditions and restrictions, if any, on the payment of
         dividends or on the making of other distributions on, or the purchase,
         redemption, or other acquisition by the Company or any subsidiary of,
         the Common Stock or of any other class (or other series of the same
         class) ranking junior to the shares of such series as to dividends or
         upon liquidation, dissolution or winding up;

            (h) The conditions and restrictions, if any, on the creation of
         indebtedness of the Company, or any subsidiary, or on the issue of any
         additional stock ranking on a parity with or prior to the shares of
         such series as to dividends or upon liquidation, dissolution or winding
         up; and

            (i) Such other powers, preferences and relative, participating,
         optional or other special rights, qualifications, limitations or
         restrictions as shall not be inconsistent with any such resolution or
         resolutions previously adopted as to shares then still outstanding or
         with the laws of the State of Delaware.

         3. CONSIDERATION FOR ISSUANCE. The authorized but unissued shares of
Common Stock and the authorized but unissued shares of Preferred Stock of the
Company may be issued for such consideration, having a value, not less than the
par value thereof (if any), as is determined from time to time by the Board of
Directors.

         4. MATTERS PERTAINING TO VOTING.

            (a) Except as otherwise determined by the provisions of this Article
         FOURTH or pursuant to authority of the Board of Directors as
         hereinbefore provided or by the General Corporation Law of the State of
         Delaware, all voting rights shall be vested exclusively in the holders
         of the outstanding shares of Common Stock and each such holder shall be
         entitled to one (1) vote per share for all purposes for such share of
         Common Stock held of record by him.

            (b) Except as otherwise determined pursuant to authority of the
         Board of Directors as hereinbefore provided, or by the General
         Corporation Law of the State of Delaware, the holders of shares of
         Preferred Stock shall not be entitled to vote for any purpose nor shall
         they be entitled to notice of meetings of stockholders.


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         FIFTH. The corporation is to have perpetual existence.

         SIXTH. Election of directors need not be by written ballot unless the
by-laws of the corporation shall so provide.

         SEVENTH. The corporation shall, to the fullest extent permitted by
Section 145 of the General Corporation Law of the State of Delaware, as that
section may be amended and supplemented from time to time, indemnify any and all
persons whom it shall have power to indemnify under that section against any
expenses, liabilities or other matters referred to in or covered by that
section. The indemnification provided for herein shall not be deemed exclusive
of any other rights to which those seeking indemnification may be entitled under
any by-law, agreement, vote of stockholders or disinterested directors or
otherwise, both as to action in their official capacities and as to action in
another capacity while holding such office, and shall continue as to a person
who has ceased to be a director, officer, employee or agent and shall inure to
the benefit of the heirs, executors and administrators of such a person.

         EIGHTH. A director of the corporation shall not be personally liable to
the corporation or its stockholders for monetary damages for breach of fiduciary
duty as a director, except for liability (i) for any breach of the director's
duty of loyalty to the corporation or its stockholders, (ii) for acts or
omissions not in good faith or which involve intentional misconduct or a knowing
violation of law, (iii) under Section 174 of the General Corporation Law of the
State of Delaware or (iv) for any transaction from which the director derived an
improper personal benefit.

         The foregoing provisions of this Article EIGHTH shall not eliminate the
liability of a director for any act or omission occurring prior to the date on
which this Article EIGHTH becomes effective.

         If the General Corporation Law of the State of Delaware is amended
after approval of this Article EIGHTH by the stockholders to authorize the
further elimination or limitation of the liability of directors, then the
liability of directors shall be eliminated or limited to the full extent
authorized by the General Corporation Law of the State of Delaware, as so
amended.

         Any repeal or modification of this Article EIGHTH shall not adversely
affect any right or protection of a director of the corporation existing at the
time of such repeal or modification.

         NINTH. The corporation reserves the right to amend, alter, change or
repeal any provision contained in this Certificate of Incorporation, in the
manner now or hereafter prescribed by statute, and all rights conferred upon
stockholders herein are granted subject to this reservation

         TENTH. This Restated Certificate of Incorporation has been duly adopted
by the Board of Directors of the corporation in accordance with the provisions
of Section 245 of the Delaware General Corporation Law. This Restated
Certificate of Incorporation only restates and integrates, and does not further
amend, the provisions of the corporation's Certificate of Incorporation as
heretofore amended or supplemented, and there is no discrepancy between those
provisions and the provisions of this Restated Certificate of Incorporation.

         Signed this 30th day of June, 1992.


                                        /s/ Sandford D. Smith
                                        --------------------------------------
                                         Sandford D. Smith,
Attest:                                  President and Chief Executive Officer
/s/ Ramesh L. Ratan
- -------------------------------
Ramesh L. Ratan
Senior Vice President,
Administration, Chief
Financial Officer and Secretary


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                            CERTIFICATE OF AMENDMENT

                                       OF

                          CERTIFICATE OF INCORPORATION

         Repligen Corporation, a corporation organized and existing under and by
virtue of the General Corporation Law of the State of Delaware ("DGCL"), DOES
HEREBY CERTIFY pursuant to Section 242 of the DGCL:

         FIRST: That the Board of Directors of Repligen Corporation (the
"Corporation"), by unanimous written consent dated June 21, 1999 in accordance
with the provisions of Sections 141(f) and 242 of the DGCL, duly and validly
adopted the following resolutions:

RESOLVED:     To amend, restate or amend and restate the Certificate of
              Incorporation to allow the Company the authority to issue
              forty-five million (45,000,000) shares of capital stock, of which
              forty million (40,000,000) shares shall constitute Common Stock
              ("Common Stock"), each share having a par value of one cent, and
              five million (5,000,000) shares shall constitute Preferred Stock
              ("Preferred Stock"), each such share having a par value of one
              cent.

RESOLVED:     That the Board of Directors deems the proposal set forth
              immediately above advisable and in the best interest of the
              Corporation and its stockholders; and that the approval of such
              proposal be recommended to the stockholders for approval at the
              Annual Meeting of Stockholders of the Corporation.

RESOLVED:     That the officers of the Corporation hereby are and each of them
              hereby is authorized to execute all such instruments, make all
              such payments and do all such other acts and things as in their
              opinion, or in the opinion of any of them, may be necessary or
              appropriate in order to carry out the intent and purposes of the
              foregoing resolutions.

         SECOND: That the stockholders of the Corporation duly adopted such
resolutions stated immediately above and approved of the amendment to the
Certificate of Incorporation of the Corporation by a vote of the stockholders of
the Corporation at the Annual Meeting of Stockholders held on September 16,
1999, in accordance with the provisions of Section 242 of the DGCL.

         THIRD: That the aforesaid amendment was duly adopted by such written
consent of the Board of Directors of the Corporation and by a vote of the
stockholders of the Corporation in accordance with the applicable provisions of
Section 242 of the DGCL, and the first paragraph of Article Fourth of the
Certificate of Incorporation is hereby deleted in its entirety and replaced in
its entirety to read as follows:

 "FOURTH. The total number of shares of stock which the Company shall have
 authority to issue is forty-five million (45,000,000), of which forty million
 (40,000,000) shares shall constitute Common Stock ("Common Stock"), each such
 share having a par value of one cent, and five million (5,000,000) shares shall
 constitute Preferred Stock ("Preferred Stock"), each such share having a par
 value of one cent."


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         IN WITNESS WHEREOF, said Repligen Corporation has caused this
certificate to be executed by Walter C. Herlihy, its President and Chief
Executive Officer, and attested to by Barbara Burnim-Day, its Director of
Finance, on this 17th day of September, 1999.

                                REPLIGEN CORPORATION


                                By:  /s/ Walter C. Herlihy
                                     -------------------------------------
                                     Walter C. Herlihy
                                     President and Chief Executive Officer

ATTEST:


By:   /s/ Barbara Burnim Day
      ----------------------
      Barbara Burnim Day
      Director of Finance


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