Exhibit 3.1


                         CERTIFICATE OF INCORPORATION

                                      OF

                                 MAXYGEN, INC.

     FIRST. The name of the corporation is Maxygen, Inc.
     -----

     SECOND. The address of the registered office of the corporation in the
     ------
State of Delaware is 9 East Loockerman Street, City of Dover, County of Kent.
The name of its registered agent at such address is National Corporate Research,
Ltd.

     THIRD. The nature of the business or purposes to be conducted or promoted
     -----
is to engage in any lawful act or activity for which corporations may be
organized under the General Corporation Law of the State of Delaware.

     FOURTH. The total number of shares of all classes of capital stock which
     ------
the corporation shall have authority to issue is Seventy-Five Million
(75,000,000) shares, comprised of Fifty Million (50,000,000) shares of Common
Stock with a par value of $0.0001 per share (the "Common Stock") and Twenty-Five
Million (25,000,000) shares of Preferred Stock with a par value of $0.0001 per
share (the "Preferred Stock").

     A description of the respective classes of stock and a statement of the
designations, preferences, voting powers (or no voting powers), relative,
participating, optional or other special rights and privileges and the
qualifications, limitations and restrictions of the Preferred Stock and Common
Stock are as follows:

     A.   PREFERRED STOCK
          ---------------

     The Preferred Stock may be issued in one or more series at such time or
times and for such consideration or considerations as the board of directors may
determine.  Each series shall be so designated as to distinguish the shares
thereof from the shares of all other series and classes.  Except as may be
expressly provided in this Certificate of Incorporation, including any
certificate of designations for a series of Preferred Stock, different series of
Preferred Stock shall not be construed to constitute different classes of shares
for the purpose of voting by classes.

     The board of directors is expressly authorized, subject to the limitations
prescribed by law and the provisions of this Certificate of Incorporation, to
provide for the issuance of all or any shares of the Preferred Stock, in one or
more series, each with such designations, preferences, voting powers (or no
voting powers), relative, participating, optional or other special rights and
privileges and such qualifications, limitations or restrictions thereof as shall
be stated in the resolution or resolutions adopted by the board


of directors to create such series, and a certificate of designations setting
forth a copy of said resolution or resolutions shall be filed in accordance with
the General Corporation Law of the State of Delaware. The authority of the board
of directors with respect to each such series shall include without limitation
of the foregoing the right to specify the number of shares of each such series
and to authorize an increase or decrease in such number of shares and the right
to provide that the shares of each such series may be: (i) subject to redemption
at such time or times and at such price or prices; (ii) entitled to receive
dividends (which may be cumulative or non-cumulative) at such rates, on such
conditions, and at such times, and payable in preference to, or in such relation
to, the dividends payable on any other class or classes or any other series;
(iii) entitled to such rights upon the dissolution of, or upon any distribution
of the assets of, the corporation; (iv) convertible into, or exchangeable for,
shares of any other class or classes of stock, or of any other series of the
same or any other class or classes of stock of the corporation at such price or
prices or at such rates of exchange and with such adjustments, if any; (v)
entitled to the benefit of such limitations, if any, on the issuance of
additional shares of such series or shares of any other series of Preferred
Stock; or (vi) entitled to such other preferences, powers, qualifications,
rights and privileges, all as the board of directors may deem advisable and as
are not inconsistent with law and the provisions of this Certificate of
Incorporation.

     B.   COMMON STOCK
          ------------

          1.   Relative Rights of Preferred Stock and Common Stock.  All
               ---------------------------------------------------
preferences, voting powers, relative, participating, optional or other special
rights and privileges, and qualifications, limitations, or restrictions of the
Common Stock are expressly made subject and subordinate to those that may be
fixed with respect to any shares of the Preferred Stock.

          2.   Voting Rights.  Except as otherwise required by law or this
               -------------
Certificate of Incorporation, including any certificate or designations for a
series of Preferred Stock, each holder of Common Stock shall have one vote in
respect of each share of stock held by him of record on the books of the
corporation for the election of directors and on all matters submitted to a vote
of stockholders of the corporation.

          3.   Dividends.  Subject to the preferential rights of the Preferred
               ---------
Stock, the holders of shares of Common Stock shall be entitled to receive, when
and if declared by the board of directors, out of the assets of the corporation
which are by law available therefor, dividends payable either in cash, in
property or in shares of capital stock.

          4.   Dissolution, Liquidation or Winding Up.  In the event of any
               --------------------------------------
dissolution, liquidation or winding up of the affairs of the corporation, after
distribution in full of the preferential amounts, if any, to be distributed to
the holders of shares of Preferred Stock, holders of Common Stock shall be
entitled, unless otherwise provided by

                                       2


law or this Certificate of Incorporation, including any certificate of
designations for a series of Preferred Stock, to receive all of the remaining
assets of the corporation of whatever kind available for distribution to
stockholders ratably in proportion to the number of shares of Common Stock held
by them respectively.

     FIFTH. The name and mailing address of the sole incorporator is Julian N.
     -----
Stern, Suite 1100, 525 University Avenue, Palo Alto, California 94301.

     SIXTH. The corporation is to have perpetual existence.
     -----

     SEVENTH. In furtherance and not in limitation of the powers conferred
     -------
by the laws of the State of Delaware:

     A.   The board of directors of the corporation is expressly authorized:

          (i)   To make, alter or repeal the by-laws of the corporation.

          (ii)  To authorize and cause to be executed mortgages and liens upon
the real and personal property of the corporation.

          (iii) To set apart out of any of the funds of the corporation
available for dividends a reserve or reserves for any proper purpose and to
abolish any such reserve in the manner in which it was created.

          (iv)  By a majority of the whole board, to designate one or more
committees, each committee to consist of one or more of the directors of the
corporation.  The board may designate one or more directors as alternate members
of any committee, who may replace any absent or disqualified member of any
committee.  The by-laws may provide that in the absence or disqualification of a
member of a committee, the member or members thereof present at any meeting and
not disqualified from voting, whether or not he or they constitute a quorum, may
unanimously appoint another member of the board of directors to act at the
meeting in the place of any such absent or disqualified member.  Any such
committee, to the extent provided in the resolution of the board of directors,
or in the by-laws of the corporation, shall have and may exercise all the powers
and authority of the board of directors in the management of the business and
affairs of the corporation, and may authorize the seal of the corporation to be
affixed to all papers which may require it; but no such committee shall have the
power or authority in reference to amending the Certificate of Incorporation
(except that a committee may, to the extent authorized in the resolution or
resolutions providing for the issuance of shares of stock adopted by the board
of directors as provided in Section 151(a) of the General Corporation Law of the
State of Delaware, fix any of the preferences or rights of such shares relating
to dividends, redemption, dissolution, any distribution of assets of the
corporation or the conversion into or the exchange of such shares for, shares of
any other

                                       3


class or classes or any other series of the same or any other class or classes
of stock of the corporation), adopting an agreement of merger or consolidation
under Sections 251 or 252 of the General Corporation Law of the State of
Delaware, recommending to the stockholders the sale, lease or exchange, of all
or substantially all of the corporation's property and assets, recommending to
the stockholders a dissolution of the corporation or a revocation of a
dissolution, or amending the by-laws of the corporation; and, unless the
resolution of by-laws expressly so provided, no such committee shall have the
power or authority to declare a dividend, to authorize the issuance of stock, or
to adopt a certificate of ownership and merger pursuant to Section 253 of the
General Corporation Law of the State of Delaware.

          (v)  When and as authorized by the stockholders in accordance with
statute, to sell, lease or exchange all or substantially all of the property and
assets of the corporation, including its good will and its corporate franchises,
upon such terms and conditions and for such consideration, which may consist, in
whole or in part of money or property, including shares of stock in, and/or
other securities of, any other corporation or corporations, as its board of
directors shall deem expedient and for the best interests of the corporation.

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

     C.   The books of the corporation may be kept at such place within or
without the State of Delaware as the by-laws of the corporation may provide or
as may be designated from time to time by the board of directors of the
corporation.

     EIGHTH.  Whenever a compromise or arrangement is proposed between this
     ------
corporation and its creditors or any class of them and/or between this
corporation and its stockholders or any class of them, any court of equitable
jurisdiction within the State of Delaware may, on the application or in a
summary way of this corporation or of any creditor or stockholder thereof or on
the application of any receiver or receivers appointed for this corporation
under the provisions of Section 291 of Title 8 of the Delaware Code or on the
application of trustees in dissolution or of any receiver or receivers appointed
for this corporation under the provisions of Section 279 of Title 8 of the
Delaware Code, order a meeting of the creditors or classes of creditors, and/or
of the stockholders or classes of stockholders of this corporation, as the case
may be, to be summoned in such manner as the said court directs.  If a majority
in number representing three-fourths in value of the creditors or class of
creditors, and/or of the stockholders or class of stockholders of this
corporation, as the case may be, agree to any compromise or arrangement and to
any reorganization of this corporation as a consequence of such compromise or
arrangement, the said compromise or arrangement and the said reorganization
shall, if sanctioned by the court to which the said application has been

                                       4


made, be binding on all the creditors or class of creditors, and/or on all the
stockholders or class of stockholders, of this corporation, as the case may be,
and also on this corporation.

     NINTH.  A director of this 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 act 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 any improper
personal benefit. If the Delaware General Corporation Law is amended hereafter
to authorize corporate action further eliminating or limiting the personal
liability of directors, then the liability of the director of the corporation
shall be eliminated or limited to the fullest extent permitted by the Delaware
General Corporation Law, as so amended.

     Any repeal or modification of the foregoing paragraph by the stockholders
of the corporation shall not adversely affect any right or protection of a
director of the corporation existing at the time of repeal or modification.

     TENTH.
     -----

     A.   RIGHT TO INDEMNIFICATION.
          ------------------------

     Each person who was or is made a party or is threatened to be made a party
to or is involved in any action, suit or proceeding, whether civil, criminal,
administrative or investigative ("proceeding"), by reason of the fact that he or
she or a person of whom he or she is the legal representative, is or was a
director or officer, employee or agent of the corporation or is or was serving
at the request of the corporation as a director or officer, employee or agent of
another corporation, or of a partnership, joint venture, trust or other
enterprise, including service with respect to employee benefit plans, whether
the basis of such proceeding is alleged action in an official capacity as
director, officer, employee or agent or in any other capacity while serving as a
director, officer, employee or agent, shall be indemnified and held harmless by
the corporation to the fullest extent authorized by the Delaware General
Corporation Law, as the same exists or may hereafter be amended, (but, in the
case of such amendment, only to the extent that such amendment permits the
corporation to provide broader indemnification rights than said Law permitted
the corporation to provide prior to such amendment) against all expenses,
liability and loss including attorneys' fees, judgments, fines, ERISA excise
taxes or penalties and amounts paid or to be paid in settlement) reasonably
incurred or suffered by such person in connection therewith and such
indemnification shall continue as to a person who has ceased to be a director,
officer, employee or agent and shall insure to the benefit of his or

                                       5


her heirs, executors and administrators; provided, however, that the corporation
                                         --------  -------
shall indemnify any such person seeking indemnity in connection with an action,
suit or proceeding (or part thereof) initiated by such person only if such
action, suit or proceeding (or part thereof) was authorized by the board of
directors of the corporation. Such right shall be a contract right and shall
include the right to be paid by the corporation expenses incurred in defending
any such proceeding in advance of its final disposition; provided, however, that
                                                         --------  -------
the payment of such expenses incurred by a director or officer of the
corporation in his or her capacity as a director or officer and not in any other
capacity in which service was or is rendered by such person while a director or
officer, including, without limitation service to an employee benefit plan) in
advance of the final disposition of such proceeding, shall be made only upon
delivery to the corporation of an undertaking, by or on behalf of such director
or officer, to repay all amounts so advanced if it should be determined
ultimately that such director or officer is not entitled to be indemnified under
this Section or otherwise.

     B.   RIGHT OF CLAIMANT TO BRING SUIT.
          -------------------------------

     If a claim under Paragraph A of Article TENTH is not paid in full by the
corporation within ninety (90) days after a written claim has been received by
the corporation, the claimant may at any time thereafter bring suit against the
corporation to recover the unpaid amount of the claim and, if successful in
whole or in part, the claimant shall be entitled to be paid also the expense of
prosecuting such claim.  It shall be a defense to any such action (other than an
action brought to enforce a claim for expenses incurred in defending any
proceeding in advance of its final disposition where the required undertaking,
if any, has been tendered to this corporation) that the claimant has not met the
standards of conduct which make it permissible under the Delaware General
Corporation Law for the corporation to indemnify the claimant for the amount
claimed, but the burden of proving such a defense shall be on the corporation.
Neither the failure of the corporation (including its board of directors,
independent legal counsel, or its stockholders) to have made a determination
prior to the commencement of such action that indemnification of the claimant is
proper in the circumstances because he or she has met the applicable standard of
conduct set forth in the Delaware General Corporation Law, nor an actual
determination by the corporation (including its board of directors, independent
legal counsel, or its stockholders) that the claimant has not met such
applicable standard of conduct; shall be a defense to the action or create a
presumption that claimant has not met the applicable standard of conduct.

     C.   NON-EXCLUSIVITY OF RIGHTS.
          -------------------------

     The rights conferred on any person by Paragraphs A and B of Article TENTH
shall not be exclusive of any other right which such persons may have or
hereafter acquire

                                       6


under any statute, provision of the Certificate of Incorporation, by-law,
agreement, vote of stockholders or disinterested directors or otherwise.

     D.   INSURANCE.
          ---------

     The corporation may maintain insurance, at its expense, to protect itself
and any such director, officer, employee or agent of the corporation or another
corporation, partnership, joint venture, trust or other enterprise against, any
such expense, liability, or loss, whether or not the corporation would have the
power to indemnify such person against such expense, liability or loss under the
Delaware General Corporation Law.

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

     I, the undersigned, being the sole incorporator hereinabove named, for the
purpose of forming a corporation pursuant to the General Corporation Law of the
State of Delaware, do make this certificate, hereby declaring and certifying
that this is my act and deed and the facts herein are true, and accordingly have
hereunto set my hand this 6th day of May, 1996




                                        /s/ Julian N. Stern
                                        --------------------------------------
                                        Julian N. Stern, Sole Incorporator

                                       7