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                                                                     EXHIBIT 3.1

                           CERTIFICATE OF AMENDMENT OF
              AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF
                       INTRABIOTICS PHARMACEUTICALS, INC.

         IntraBiotics Pharmaceuticals, Inc., a corporation organized and
existing under and by virtue of the General Corporation Law of the State of
Delaware (the "Corporation"), does hereby certify:

         FIRST: The name of the Corporation is IntraBiotics Pharmaceuticals,
Inc.

         SECOND: The Certificate of Incorporation of the Corporation was
originally filed with the Secretary of State of the State of Delaware on January
19, 1994.

         THIRD: The Board of Directors of the Corporation, acting in accordance
with the provisions of Sections 141 and 242 of the General Corporation Law of
the State of Delaware, adopted resolutions amending its Amended and Restated
Certificate of Incorporation as follows:

         The first paragraph of Article IV shall be amended and restated to read
in its entirety as follows:

                                      "IV.

                  A. 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 Seventy-Five Million (75,000,000) shares. Seventy Million
         (70,000,000) 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)."

         FOURTH: Thereafter, pursuant to a resolution of the Board of Directors,
this Certificate of Amendment was submitted to the stockholders of the
Corporation for approval, and was duly adopted in accordance with the provisions
of Section 242 of the General Corporation Law of the State of Delaware.

         IN WITNESS WHEREOF, IntraBiotics Pharmaceuticals, Inc. has caused this
Certificate of Amendment to be signed by its President, Chief Operating Officer
and Director on this 7th day of June, 2002.

                                    INTRABIOTICS PHARMACEUTICALS, INC.

                                    By: /s/ Ernest Mario
                                        ____________________________________
                                        Ernest Mario
                                        Chairman and Chief Executive Officer

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                              AMENDED AND RESTATED
                         CERTIFICATE OF INCORPORATION OF
                       INTRABIOTICS PHARMACEUTICALS, INC.

         The undersigned, Kenneth J. Kelley, hereby certifies that:

ONE: He is the duly elected and acting President, of said corporation, which was
originally incorporated in Delaware on January 19, 1994.

TWO: The Amended and Restated Certificate of Incorporation of said corporation
shall be amended and restated to read in full as follows:
"
                                       I.

         The name of this corporation is IntraBiotics Pharmaceuticals, Inc.

                                       II.

         The address of the registered office of the corporation in the State of
Delaware is Corporation Trust Company, 1209 Orange Street, City of Wilmington,
County of New Castle, and the name of the registered agent of the corporation in
the State of Delaware at such address is the Corporation Trust Company.

                                      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.

         A.       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 Fifty-Five Million (55,000,000) shares.
                  Fifty Million (50,000,000) 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).

         B.       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 ("DGCL"), 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

                                       2.

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                  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.

                                       V.

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:

         A.       BOARD OF DIRECTORS.

                  1.       POWERS; NUMBER OF DIRECTORS. 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.       ELECTION OF DIRECTORS. 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 (the "1933
                           Act"), 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 section, 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.

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                  3.       REMOVAL OF DIRECTORS

                           a.       Neither the Board of Directors nor any
individual director may be removed without cause.

                           b.       Subject to any limitation imposed by law,
any individual director or directors may be removed with cause by the holders of
a majority of the voting power of the corporation entitled to vote at an
election of directors.

                  4.       VACANCIES

                           a.       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 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.       If at the time of filling any vacancy or any
                                    newly created directorship, the directors
                                    then in office shall constitute less than a
                                    majority of the whole board (as constituted
                                    immediately prior to any such increase), the
                                    Delaware Court of Chancery may, upon
                                    application of any stockholder or
                                    stockholders holding at least ten percent
                                    (10%) of the total number of the shares at
                                    the time outstanding having the right to
                                    vote for such directors, summarily order an
                                    election to be held to fill any such
                                    vacancies or newly created directorships, or
                                    to replace the directors chosen by the
                                    directors then in offices as aforesaid,
                                    which election shall be governed by Section
                                    211 of the DGCL.

         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 of the corporation entitled to vote. The Board
                           of Directors shall also have the power to adopt,
                           amend, or repeal Bylaws.

                                       4.

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                  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
                           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.

                                       VI.

         A.       The liability of the directors for monetary damages shall be
                  eliminated to the fullest extent under applicable law.

         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."

                                      * * *

THREE:   This Amended and Restated Certificate of Incorporation was duly adopted
in accordance with the provisions of Section 242 and Section 245 of the General
Corporation Law of the State of Delaware, and was approved by the Board of
Directors of the Corporation and stockholders holding the requisite number of
shares required by statute, given in accordance with and pursuant to Section 141
and 228 of the General Corporation Law of the State of Delaware with written
notice given to those stockholders who did not consent as provided in said
Section 228.

                                       5.

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         IN WITNESS WHEREOF, this Amended and Restated Certificate of
Incorporation has been subscribed this 31 day of March, 2000 by the undersigned
who affirms that the statements made herein are true and correct.

                                    INTRABIOTICS PHARMACEUTICALS, INC.

                                    By: /s/ Kenneth J. Kelley
                                        _______________________________________
                                         Kenneth J. Kelley
                                         President and Chief Executive Officer

                                       6.