RESTATED
                                        
                         CERTIFICATE OF INCORPORATION
                                        
                                      OF
                                        
                        ALBANY MOLECULAR RESEARCH, INC.
 
 
     ALBANY MOLECULAR RESEARCH, INC., a corporation organized and existing under
the laws of the State of Delaware (the "Corporation"), hereby certifies as
follows:
 
     1.  The name of the Corporation is Albany Molecular Research, Inc.  The
date of the filing of its original Certificate of Incorporation with the
Secretary of State of the State of Delaware was August 6, 1998.
 
     2.  This Restated Certificate of Incorporation restates and integrates, but
does not further amend, the provisions of the Amended and Restated Certificate
of Incorporation of the Corporation filed with the Secretary of State of the
State of Delaware on February 3, 1999, as heretofore amended (the
"Certificate"), and there is no discrepancy between those provisions and the
provisions of this Restated Certificate of Incorporation.  This Restated
Certificate of Incorporation was duly adopted by the Board of Directors in
accordance with the provisions of Section 245 of the General Corporation Law of
the State of Delaware (the "DGCL").
 
     3.  The text of the Certificate is hereby restated in its entirety to
provide as herein set forth in full.
 
 
                                   ARTICLE I
                                   ---------
                                        
                                      NAME
                                      ----
 
     The name of the Corporation is Albany Molecular Research, Inc.
 
 
                                   ARTICLE II
                                   ----------
                                        
                               REGISTERED OFFICE
                               -----------------
 
     The address of the Corporation's registered office in the State of Delaware
is Corporation Trust Center, 1209 Orange Street, Wilmington, Delaware, County of
New Castle.  The name of its registered agent at such address is The Corporation
Trust Company.
 
<PAGE>
 
                                  ARTICLE III
                                  -----------
                                        
                                    PURPOSE
                                    -------
 
     The nature of the business or purposes to be conducted or promoted by the
Corporation is to engage in any lawful act or activity for which corporations
may be organized under the DGCL.
 
 
                                  ARTICLE IV
                                  ----------
                                        
                                 CAPITAL STOCK
                                 -------------
 
     The total number of shares of capital stock which the Corporation shall
have authority to issue is Fifty-Two Million (52,000,000) shares, of which (a)
Fifty Million (50,000,000) shares shall be common stock, par value $.01 per
share (the "Common Stock"), and (b) Two Million (2,000,000) shares shall be
undesignated preferred stock, par value $.01 per share (the "Undesignated
Preferred Stock").
 
     Except as otherwise restricted by this Restated Certificate of
Incorporation, the Corporation is authorized to issue, from time to time, all or
any portion of the capital stock of the Corporation which may have been
authorized but not issued, to such person or persons and for such lawful
consideration as it may deem appropriate, and generally in its absolute
discretion to determine the terms and manner of any disposition of such
authorized but unissued capital stock.
 
     Any and all such shares issued for which the full consideration has been
paid or delivered shall be deemed fully paid shares of capital stock, and the
holder of such shares shall not be liable for any further call or assessment or
any other payment thereon.
 
     The number of authorized shares of the class of Undesignated Preferred
Stock may from time to time be increased or decreased (but not below the number
of shares outstanding) by the affirmative vote of the holders of a majority of
the shares of Common Stock entitled to vote, without a vote of the holders of
the Undesignated Preferred Stock.
 
     The designations, powers, preferences and rights of, and the
qualifications, limitations and restrictions upon, each class or series of stock
shall be determined in accordance with, or as set forth below in, this Article
IV.
 
<PAGE>
 
                                A.  COMMON STOCK
                                    ------------
 
     1.  Designation; Ranking.  A total of 50,000,000 shares of the
         --------------------                                      
Corporation's common stock shall be designated as Common Stock, $.01 par value
per share (the "Common Stock").
 
     2.  Voting.
         ------ 
 
         (a)  Election of Directors.  The holders of Common Stock shall be 
              ---------------------        
     entitled to elect all of the Directors of the Corporation. Such Directors
     shall be the candidates receiving the highest number of affirmative votes
     entitled to be cast (with each holder entitled to cast one vote for or
     against each candidate with respect to each share held by such holder),
     with votes cast against such candidates and votes withheld having no legal
     effect. The election of such Directors shall occur at the annual meeting of
     holders of capital stock or at any special meeting called and held in
     accordance with the By-laws of the Corporation. If a person elected in
     accordance with the foregoing provisions should cease to be a Director for
     any reason, the vacancy shall only be filled by the vote or written consent
     of holders of the outstanding shares entitled to vote for such Directors,
     in the manner and on the basis specified above.
 
         (b)  Other Voting.  The holder of each share of Common Stock shall be
              ------------                                                    
     entitled to one vote for each such share as determined on the record date
     for the vote or consent of stockholders upon any items submitted to a vote
     of stockholders.
 
     3.  Dividends.  The holders of Common Stock shall be entitled to receive
         ---------                                                           
dividends out of funds legally available therefor at such times and in such
amounts as the Board of Directors may determine in its sole discretion.
 
     4.  Liquidation.  Upon any liquidation, dissolution or winding up of the
         -----------                                                         
Corporation and its subsidiaries, whether voluntary or involuntary, after the
payment or provision for payment of all debts and liabilities of the
Corporation, the holders of Common Stock shall be entitled to share ratably in
the remaining assets of the Corporation available for distribution.
 
 
                        B.  UNDESIGNATED PREFERRED STOCK
                            ----------------------------
 
     1.  Authority to Issue.  Subject to any limitations prescribed by law, the
         ------------------                                                    
Board of Directors or any authorized committee thereof is expressly authorized
to provide for the issuance of the shares of Undesignated Preferred Stock in one
or more series of such stock, and by filing a certificate pursuant to applicable
law of the State of Delaware, to establish or change from time to time the
number of shares to be included in each such series, and to fix the
designations, powers, preferences and the relative, participating, optional or
other special rights of the shares of each series and any 
 
<PAGE>
 
qualifications, limitations and restrictions thereof. Any action by the Board of
Directors or any authorized committee thereof under this Article B shall require
the affirmative vote of a majority of the Directors then in office or a majority
of the members of such committee.
 
     2.  Powers, Preferences, Rights, Qualifications, Limitations and
         ------------------------------------------------------------
Restriction of Each Series of Undesignated Preferred Stock.  The Board of
- ----------------------------------------------------------               
Directors or any authorized committee thereof shall have the right to determine
or fix one or more of the following with respect to each series of Undesignated
Preferred Stock to the fullest extent permitted by law:
 
         (a)   The distinctive serial designation and the number of shares
     constituting such series;
 
         (b)   The dividend rates or the amount of dividends to be paid on the
     shares of such series, whether dividends shall be cumulative and, if so,
     from which date or dates, the payment date or dates for dividends, and the
     participating and other rights, if any, with respect to dividends;
 
         (c)   The voting rights and powers, full or limited, if any, of the
     shares of such series;
 
         (d)   Whether the shares of such series shall be redeemable and, if so,
     the price or prices at which, and the terms and conditions on which, such
     shares may be redeemed;
 
         (e)   The amount or amounts payable upon the shares of such series and
     any preferences applicable thereto in the event of voluntary or involuntary
     liquidation, dissolution or winding up of the Corporation;
 
         (f)   Whether the shares of such series shall be entitled to the
     benefit of a sinking or retirement fund to be applied to the purchase or
     redemption of such shares, and if so entitled, the amount of such fund and
     the manner of its application, including the price or prices at which such
     shares may be redeemed or purchased through the application of such fund;
 
         (g)   Whether the shares of such series shall be convertible into, or
     exchangeable for, shares of any other class or classes or of any other
     series of the same or any other class or classes of stock of the
     Corporation and, if so convertible or exchangeable, the conversion price or
     prices, or the rate or rates of exchange, and the adjustments thereof, if
     any, at which such conversion or exchange may be made, and any other terms
     and conditions of such conversion or exchange;
 
         (h)   The consideration for which the shares of such series shall be
     issued;
 
<PAGE>
 
         (i)   Whether the shares of such series which are redeemed or converted
     shall have the status of authorized but unissued shares of Undesignated
     Preferred Stock (or series thereof) and whether such shares may be reissued
     as shares of the same or any other class or series of stock; and
 
         (j)   Such other powers, preferences, rights, qualifications,
     limitations and restrictions thereof as the Board of Directors or any
     authorized committee thereof may deem advisable.
 
 
                                   ARTICLE V
                                   ---------
                                        
                              STOCKHOLDER ACTION
                              ------------------
 
     Any action required or permitted to be taken by the stockholders of the
Corporation at any annual or special meeting of stockholders of the Corporation
must be effected at a duly called annual or special meeting of stockholders and
may not be taken or effected by a written consent of stockholders in lieu
thereof.
 
 
                                  ARTICLE VI
                                  ----------
                                        
                                   DIRECTORS
                                   ---------
 
     1.  General.  The business and affairs of the Corporation shall be managed
         -------                                                               
by or under the direction of the Board of Directors except as otherwise provided
herein or required by law.
 
     2.  Election of Directors.  Election of Directors need not be by written
         ---------------------                                               
ballot unless the By-laws of the Corporation shall so provide.
 
<PAGE>
 
     3.  Terms of Directors.  The number of Directors of the Corporation shall
         ------------------                                                   
be fixed by resolution duly adopted from time to time by the Board of Directors.
The Directors, other than those who may be elected by the holders of any series
of Undesignated Preferred Stock of the Corporation, shall be classified, with
respect to the term for which they severally hold office, into three classes, as
nearly equal in number as possible.  The initial Class I Directors of the
Corporation shall be Chester J. Opalka and Frank W. Haydu III; the initial Class
II Director of the Corporation shall be Donald E. Kuhla, Ph.D.; and the initial
Class III Directors of the Corporation shall be Thomas E. D'Ambra, Ph.D. and
Anthony P. Tartaglia, M.D.  The initial Class I Directors shall serve for a term
expiring at the annual meeting of stockholders to be held in 1999, the initial
Class II Director shall serve for a term expiring at the annual meeting of
stockholders to be held in 2000, and the initial Class III Directors shall serve
for a term expiring at the annual meeting of stockholders to be held in 2001.
At each annual meeting of stockholders, the successor or successors of the class
of Directors whose term expires at that meeting shall be elected by a plurality
of the votes cast at such meeting and shall hold office for a term expiring at
the annual meeting of stockholders held in the third year following the year of
their election.  The Directors elected to each class shall hold office until
their successors are duly elected and qualified or until their earlier
resignation or removal.
 
     Notwithstanding the foregoing, whenever, pursuant to the provisions of
Article IV of this Restated Certificate of Incorporation, the holders of any one
or more series of Undesignated Preferred Stock shall have the right, voting
separately as a series or together with holders of other such series, to elect
Directors at an annual or special meeting of stockholders, the election, term of
office, filling of vacancies and other features of such directorships shall be
governed by the terms of this Restated Certificate of Incorporation and any
certificate of designations applicable thereto, and such Directors so elected
shall not be divided into classes pursuant to this Article VI.3.
 
     During any period when the holders of any series of Undesignated Preferred
Stock have the right to elect additional Directors as provided for or fixed
pursuant to the provisions of Article IV hereof, then upon commencement and for
the duration of the period during which such right continues:  (i) the then
otherwise total authorized number of Directors of the Corporation shall
automatically be increased by such specified number of Directors, and the
holders of such Undesignated Preferred Stock shall be entitled to elect the
additional Directors so provided for or fixed pursuant to said provisions, and
(ii) each such additional Director shall serve until such Director's successor
shall have been duly elected and qualified, or until such Director's right to
hold such office terminates pursuant to said provisions, whichever occurs
earlier, subject to such Director's earlier death, disqualification, resignation
or removal.  Except as otherwise provided by the Board of Directors in the
resolution or resolutions establishing such series, whenever the holders of any
series of Undesignated Preferred Stock having such right to elect additional
Directors are divested of such right pursuant to the provisions of such stock,
the terms of office of all such additional Directors elected by the holders of
such stock, or elected to fill any vacancies resulting from the death,
resignation, disqualification or removal of such additional Directors, shall
automatically terminate and the total and authorized number of Directors of the
Corporation shall be reduced accordingly.
 
<PAGE>
 
     4.  Vacancies.  Subject to the rights, if any, of the holders of any series
         ---------                                                              
of Undesignated Preferred Stock to elect Directors and to fill vacancies in the
Board of Directors relating thereto, any and all vacancies in the Board of
Directors, however occurring, including, without limitation, by reason of an
increase in size of the Board of Directors, or the death, resignation,
disqualification or removal of a Director, shall be filled solely by the
affirmative vote of a majority of the remaining Directors then in office, even
if less than a quorum of the Board of Directors.  Any Director appointed in
accordance with the preceding sentence shall hold office for the remainder of
the full term of the class of Directors in which the new directorship was
created or the vacancy occurred and until such Director's successor shall have
been duly elected and qualified or until his or her earlier resignation or
removal.  Subject to the rights, if any, of the holders of any series of
Undesignated Preferred Stock to elect Directors, when the number of Directors is
increased or decreased, the Board of Directors shall determine the class or
classes to which the increased or decreased number of Directors shall be
apportioned; provided, however, that no decrease in the number of Directors
             --------  -------                                             
shall shorten the term of any incumbent Director.  In the event of a vacancy in
the Board of Directors, the remaining Directors, except as otherwise provided by
law, may exercise the powers of the full Board of Directors until the vacancy is
filled.
 
     5.  Removal.  Subject to the rights, if any, of any series of Undesignated
         -------                                                               
Preferred Stock to elect Directors and to remove any Director whom the holders
of any such stock have the right to elect, any Director (including persons
elected by Directors to fill vacancies in the Board of Directors) may be removed
from office (i) only with cause and (ii) only by the affirmative vote of at
least two-thirds of the total votes which would be eligible to be cast by
stockholders in the election of such Director.  At least thirty (30) days prior
to any meeting of stockholders at which it is proposed that any Director be
removed from office, written notice of such proposed removal shall be sent to
the Director whose removal will be considered at the meeting.  For purposes of
this Restated Certificate of Incorporation, "cause," with respect to the removal
of any Director, shall mean only (i) conviction of a felony, (ii) declaration of
unsound mind by order of court, (iii) gross dereliction of duty, (iv) commission
of any action involving moral turpitude, or (v) commission of an action which
constitutes intentional misconduct or a knowing violation of law if such action
in either event results both in an improper substantial personal benefit and a
material injury to the Corporation.
 
 
                                  ARTICLE VII
                                  -----------
                                        
                            LIMITATION OF LIABILITY
                            -----------------------
 
     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 (a) for any breach of the Director's
duty of loyalty to the 
 
<PAGE>
 
Corporation or its stockholders, (b) for acts or omissions not in good faith or
which involve intentional misconduct or a knowing violation of law, (c) under
Section 174 of the DGCL or (d) for any transaction from which the Director
derived an improper personal benefit. If the DGCL is amended after the effective
date of this Restated Certificate of Incorporation to authorize corporate action
further eliminating or limiting the personal liability of Directors, then the
liability of a Director of the Corporation shall be eliminated or limited to the
fullest extent permitted by the DGCL, as so amended.
 
     Any repeal or modification of this Article VII by either of (i) the
stockholders of the Corporation or (ii) an amendment to the DGCL, shall not
adversely affect any right or protection existing at the time of such repeal or
modification with respect to any acts or omissions occurring before such repeal
or modification of a person serving as a Director at the time of such repeal or
modification.
 
                                  ARTICLE VIII
                                  ------------
                                        
                              AMENDMENT OF BY-LAWS
                              --------------------
 
     1.  Amendment by Directors.  Except as otherwise provided by law, the By-
         ----------------------                                              
laws of the Corporation may be amended or repealed by the Board of Directors by
the affirmative vote of a majority of the Directors then in office.
 
     2.  Amendment by Stockholders.  The By-laws of the Corporation may be
         -------------------------                                        
amended or repealed at any annual meeting of stockholders, or special meeting of
stockholders called for such purpose as provided in the By-laws, by the
affirmative vote of at least two-thirds of the total votes eligible to be cast
on such amendment or repeal by holders of voting stock, voting together as a
single class; provided, however, that if the Board of Directors recommends that
              --------  -------                                                
stockholders approve such amendment or repeal at such meeting of stockholders,
such amendment or repeal shall only require the affirmative vote of a majority
of the total votes eligible to be cast on such amendment or repeal by holders of
voting stock, voting together as a single class.
 
<PAGE>
 
                                   ARTICLE IX
                                   ----------
                                        
                   AMENDMENT OF CERTIFICATE OF INCORPORATION
                   -----------------------------------------
 
     The Corporation reserves the right to amend or repeal this Restated
Certificate of Incorporation in the manner now or hereafter prescribed by
statute and this Restated Certificate of Incorporation, and all rights conferred
upon stockholders herein, are granted subject to this reservation.  No amendment
or repeal of this Restated Certificate of Incorporation shall be made unless the
same is first approved by the Board of Directors pursuant to a resolution
adopted by the Board of Directors in accordance with Section 242 of the DGCL,
and, except as otherwise provided by law, thereafter approved by the
stockholders.  Whenever any vote of the holders of voting stock is required, and
in addition to any other vote of holders of voting stock that is required by
this Restated Certificate of Incorporation or by law, the affirmative vote of a
majority of the total votes eligible to be cast by holders of voting stock with
respect to such amendment or repeal, voting together as a single class, at a
duly constituted meeting of stockholders called expressly for such purpose shall
be required to amend or repeal any provisions of this Restated Certificate of
Incorporation; provided, however, that the affirmative vote of not less than 80%
               --------  -------                                                
of the total votes eligible to be cast by holders of voting stock, voting
together as a single class, shall be required to amend or repeal any of the
provisions of Article V, Article VI, Article VII or Article IX of this Restated
Certificate of Incorporation.
 
<PAGE>
 
       THIS RESTATED CERTIFICATE OF INCORPORATION is executed as of this 10th
       ----------------------------------------------------------------------
day of February, 1999.
- ----------------------
 
                                     ALBANY MOLECULAR RESEARCH, INC.
                                     -------------------------------
 
 
 
                                 By: /s/ Thomas E. D'Ambra
                                    -------------------------
                                    Thomas E. D'Ambra, Ph.D.
                                    Chairman of the Board and
                                    Chief Executive Officer