<PAGE>

                                                             Exhibit 3.1


                        STATE OF DELAWARE

                  OFFICE OF THE SECRETARY OF STATE


     I, EDWARD J. FREEL, SECRETARY OF STATE OF THE STATE OF DELAWARE, DO 
HEREBY CERTIFY THE ATTACHED IS A TRUE AND CORRECT COPY OF THE RESTATED 
CERTIFICATE OF "AVIRON", FILED IN THIS OFFICE ON THE TWENTY-SECOND DAY OF 
NOVEMBER, A.D. 1996, AT 9 O'CLOCK A.M.


                                    /S/ EDWARD J. FREEL
                     [SEAL]      ------------------------------------
                                 EDWARD J. FREEL, SECRETARY OF STATE


                                 AUTHENTICATION:   8225359

                                           DATE:   12-06-96
<PAGE>

                       AMENDED AND RESTATED
                   CERTIFICATE OF INCORPORATION
                                OF
                              AVIRON


     AVIRON, a corporation organized and existing under the laws of the state 
of Delaware (the "Corporation") hereby certifies that:

     1.   The name of the Corporation is Aviron.  The corporation was 
originally incorporated under the name Aviron Merger Corporation.

     2.   The date of filing of the Corporation's original Certificate of 
Incorporation was March 7, 1996.

     3.   The Amended and Restated Certificate of Incorporation of the 
Corporation as provided in Exhibit A hereto was duly adopted in accordance 
with the provisions of Section 242 and Section 245 of the General Corporation 
Law of the State of Delaware by the Board of Directors of the corporation.  

     4.   Pursuant to Section 245 of the Delaware General Corporation Law, 
approval of the stockholders of the corporation has been obtained.  

     5.   The Amended and Restated Certificate of Incorporation so adopted 
reads in full as set forth in Exhibit A attached hereto and is hereby 
incorporated by reference.

     IN WITNESS WHEREOF, the undersigned have signed this certificate this 
8th day of November, 1996, and hereby affirm and acknowledge under penalty of 
perjury that the filing of this Restated Certificate of Incorporation is the 
act and deed of Aviron.

                              AVIRON



                              By /s/ J. Leighton Read
                                 --------------------------------
                                 J. Leighton Read
                                 Chief Executive Officer

ATTEST:


/s/ Alan C. Mendelson
-----------------------------
Alan C. Mendelson
Secretary

<PAGE>


                       AMENDED AND RESTATED             Exhibit A
                   CERTIFICATE OF INCORPORATION
                                OF
                              AVIRON


                                I.

     The name of this corporation is Aviron.

                               II.

     The address of the registered office of the corporation in the State of 
Delaware is 1013 Centre Road, City of Wilmington, 19805, County of New Castle 
and the name of the name of the registered agent of the corporation in the 
State of Delaware at such address is The Prentice-Hall Corporation System, 
Inc.  
 
                               III.

     The purpose of this corporation is to engage in any lawful act or 
activity for which a corporation may be organized under the General 
Corporation Law of the State of Delaware.

                              IV.

          This corporation is authorized to issue two classes of stock to be 
designated, respectively, "Common Stock" and "Preferred Stock."  The total 
number of shares which the corporation is authorized to issue is Thirty Five 
Million (35,000,000) shares.  Thirty Million (30,000,000) shares shall be 
Common Stock, each having a par value of one tenth of one cent ($.001).  Five 
Million (5,000,000) shares shall be Preferred Stock, each having a par value 
of one tenth of one cent ($.001).

       The Preferred Stock may be issued from time to time in one or more 
series.  The Board of Directors is hereby authorized, by filing a certificate 
(a "Preferred Stock Designation") pursuant to the Delaware General 
Corporation Law, to fix or alter from time to time the designation, powers, 
preferences and rights of the shares of each such series and the 
qualifications, limitations or restrictions of any wholly unissued series of 
Preferred Stock, and to establish from time to time the number of shares 
constituting any such series or any of them; and to increase or decrease the 
number of shares of any series subsequent to the issuance of shares of that 
series, but not below the number of shares of such series then outstanding.  
In case the number of shares of any series shall be decreased in accordance 
with the foregoing sentence, the shares constituting such decrease shall 
resume the status that they had prior to the adoption of the resolution 
originally fixing the number of shares of such series.

                                1.


<PAGE>


                                V.

     A.   For the management of the business and for the conduct of the 
affairs of the Corporation, and in further definition, limitation and 
regulation of the powers of the Corporation, of its directors and of its 
stockholders or any class thereof, as the case may be, it is further provided 
that:

          (1)  The management of the business and the conduct of the affairs 
of the Corporation shall be vested in its Board of Directors.  The number of 
directors which shall constitute the whole Board of Directors shall be fixed 
exclusively by one or more resolutions adopted by the Board of Directors.

          (2)  Subject to the rights of the holders of any series of 
Preferred Stock to elect additional directors under specified circumstances, 
following the closing of the initial public offering pursuant to an effective 
registration statement under the Securities Act of 1933, as amended, covering 
the offer and sale of Common Stock to the public (the "Initial Public 
Offering"), the directors shall be divided into three classes designated as 
Class I, Class II and Class III, respectively.  Directors shall be assigned 
to each class in accordance with a resolution or resolutions adopted by the 
Board of Directors.  At the first annual meeting of stockholders following 
the closing of the Initial Public Offering, the term of office of the Class I 
directors shall expire and Class I directors shall be elected for a full term 
of three years.  At the second annual meeting of stockholders following the 
Closing of the Initial Public Offering, the term of office of the Class II 
directors shall expire and Class II directors shall be elected for a full 
term of three years.  At the third annual meeting of stockholders following 
the Closing of the Initial Public Offering, the term of office of the Class 
III directors shall expire and Class III directors shall be elected for a 
full term of three years.  At each succeeding annual meeting of stockholders, 
directors shall be elected for a full term of three years to succeed the 
directors of the class whose terms expire at such annual meeting.

     Notwithstanding the foregoing provisions of this Article, each director 
shall serve until his successor is duly elected and qualified or until his 
death, resignation or removal.  No decrease in the number of directors 
constituting the Board of Directors shall shorten the term of any incumbent 
director.

          (3)  Subject to the rights of the holders of any series of 
Preferred Stock, the Board of Directors or any individual director may be 
removed from office at any time (i) with cause by the affirmative vote of the 
holders of a majority of the voting power of all the then-outstanding shares 
of voting stock of the Corporation, entitled to vote at an election of 
directors (the "Voting Stock") or (ii) without cause by the affirmative vote 
of the holders of at least sixty-six and two-thirds percent (66 2/3%) of the 
voting power of all the then-outstanding shares of the Voting Stock.

          (4)  Subject to the rights of the holders of any series of 
Preferred Stock, any vacancies on the Board of Directors resulting from 
death, resignation, disqualification, removal or other causes and any newly 
created directorships resulting from any increase in the number


                                   2.

<PAGE>

of directors, shall, unless the Board of Directors determines by resolution 
that any such vacancies or newly created directorships shall be filled by the 
stockholders, except as otherwise provided by law, be filled only by the 
affirmative vote of a majority of the directors then in office, even though 
less than a quorum of the Board of Directors, and not by the stockholders.  
Any director elected in accordance with the preceding sentence shall hold 
office for the remainder of the full term of the director for which the 
vacancy was created or occurred and until such director's successor shall 
have been elected and qualified. 

     B.   (1)  Subject to paragraph (h) of Section 43 of the Bylaws, the 
Bylaws may be altered or amended or new Bylaws adopted by the affirmative 
vote of at least sixty-six and two-thirds percent (66-2/3%) of the voting 
power of all of the then-outstanding shares of the Voting Stock.  The Board 
of Directors shall also have the power to adopt, amend, or repeal Bylaws.

          (2)  The directors of the Corporation need not be elected by 
written ballot unless the Bylaws so provide.

          (3)  No action shall be taken by the stockholders of the 
Corporation except at an annual or special meeting of stockholders called in 
accordance with the Bylaws and following the closing of the Initial Public 
Offering no action shall be taken by the stockholders by written consent.

          (4)  Advance notice of stockholder nominations for the election of 
directors and of business to be brought by stockholders before any meeting of 
the stockholders of the Corporation shall be given in the manner provided in 
the Bylaws of the Corporation.

          (5)  Special meetings of the stockholders of the Corporation may be 
called, for any purpose or purposes, by (i) the Chairman of the Board of 
Directors, (ii) the President, (iii) the Board of Directors pursuant to a 
resolution adopted by a majority of the total number of authorized directors 
(whether or not there exist any vacancies in previously authorized 
directorships at the time any such resolution is presented to the Board of 
Directors for adoption) or (iv) by the holders of the shares entitled to cast 
not less that ten percent (10%) of the votes at the meeting, and shall be 
held at such place, on such date, and at such time as the Board of Directors 
shall fix.

                               VI.

     A.   A director of the Corporation shall not be personally liable to the 
Corporation or its stockholders for monetary damages for any 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 Delaware 
General Corporation Law, or (iv) for any transaction from which the director 
derived an improper personal benefit.  If the Delaware General Corporation 
Law is amended after approval by the stockholders of this Article to 
authorize corporate action further eliminating or limiting the personal 
liability of directors, then


                                  3.
<PAGE>

the liability of a director shall be eliminated or limited to the fullest 
extent permitted by the Delaware General corporation Law, as so amended.

     B.   Any repeal or modification of this Article VI shall be prospective 
and shall not affect the rights under this Article VI in effect at the time 
of the alleged occurrence of any act or omission to act giving rise to 
liability or indemnification.

                               VII.

     A.   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, except as provided in 
paragraph B. of this Article VII, and all rights conferred upon the 
stockholders herein are granted subject to this reservation. 

     B.   Notwithstanding any other provisions of this Certificate of 
Incorporation or any provision of law which might otherwise permit a lesser 
vote or no vote, but in addition to any affirmative vote of the holders of 
any particular class or series of the Voting Stock required by law, this 
Certificate of Incorporation or any Preferred Stock Designation, the 
affirmative vote of the holders of at least sixty-six and two-thirds percent 
(66-2/3%) of the voting power of all of the then-outstanding shares of the 
Voting Stock, voting together as a single class, shall be required to alter, 
amend or repeal Articles V, VI, and VII. 




                                    4.