
<PAGE>

                                                                     EXHIBIT 3.2

                              AMENDED AND RESTATED
                          CERTIFICATE OF INCORPORATION
                                       OF
                                  AEROGEN, INC.


         AEROGEN, INC., 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 AeroGen, Inc. The name under which
this corporation was originally incorporated is AeroGen, Inc.

         2. The date of filing of the Corporation's original Certificate of
Incorporation was March 12, 1998.

         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 has signed this certificate this
___ day of ______, 2000, and hereby affirms and acknowledges under penalty of
perjury that the filing of this Amended and Restated Certificate of
Incorporation is the act and deed of AeroGen, Inc.

                                              AEROGEN,  INC.



                                              By
                                                -------------------------------
                                                    Jane E. Shaw
                                                    Chief Executive Officer


                                       1.
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                                                                      EXHIBIT A

                AMENDED AND RESTATED CERTIFICATE OF INCORPORATION
                                OF AEROGEN, INC.
                             A DELAWARE CORPORATION

                                   ARTICLE I.

         The name of the corporation is AEROGEN, INC.

                                  ARTICLE II.

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

                                  ARTICLE 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 Delaware ("DGCL").

                                  ARTICLE IV.

     A. CLASSES OF STOCK. 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 One
Hundred Million (100,000,000), of which Ninety Five Million (95,000,000)
shares shall be Common Stock, par value $0.001 per share, and Five Million
(5,000,000) shares shall be Preferred Stock, par value $0.001 per share.

     B. RIGHTS, PREFERENCES AND RESTRICTIONS OF PREFERRED STOCK. 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 DGCL, to fix or alter from time to time the
designation, powers, preferences and rights (voting or otherwise) granted
upon, 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.

                                   ARTICLE 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:


                                       2.
<PAGE>

     A. MANAGEMENT OF BUSINESS. 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.

     B. BOARD OF DIRECTORS.

          1. Subject to the rights of the holders of any series of Preferred
Stock to elect additional directors under specified circumstances, 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 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 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 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
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. During such time or times that the
corporation is subject to Section 2115(b) of the California General
Corporation Law ("CGCL"), this Section B.1. of this Article V shall become
effective and be applicable only when the corporation is a "listed"
corporation within the meaning of Section 301.5 of the CGCL.

          2. In the event that the corporation is subject to Section 2115(b)
of the CGCL AND is not a "listed" corporation or ceases to be a "listed"
corporation under Section 301.5 of the CGCL, Section B.1. of this Article V
shall not apply and all directors shall be shall be elected at each annual
meeting of stockholders to hold office until the next annual meeting.

          3. No person entitled to vote at an election for directors may
cumulate votes to which such person is entitled, unless, at the time of such
election, the corporation is subject to Section 2115(b) of the CGCL AND is not
a "listed" corporation or ceases to be a "listed" corporation under Section
301.5 of the CGCL. During this time, every stockholder entitled to vote at an
election for directors may cumulate such stockholder's votes and give one
candidate a number of votes equal to the number of directors to be elected
multiplied by the number of votes to which such stockholder's shares are
otherwise entitled, or distribute the stockholder's votes on the same
principle among as many candidates as such stockholder thinks fit. No
stockholder, however, shall be entitled to so cumulate such stockholder's
votes unless (i) the names of such candidate or candidates have been placed in
nomination prior to the voting and (ii) the stockholder has given notice at
the meeting, prior to the voting, of such stockholder's intention to cumulate
such stockholder's votes. If any stockholder has given proper notice to
cumulate votes, all stockholders may cumulate their votes for any candidates
who have been properly placed in nomination. Under cumulative voting, the
candidates receiving the highest number of votes, up to the number of
directors to be elected, are elected.


                                       3.
<PAGE>

     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.

     C. REMOVAL OF DIRECTORS.

          1. During such time or times that the corporation is subject to
Section 2115(b) of the CGCL, the Board of Directors or any individual director
may be removed from office at any time without cause by the affirmative vote
of the holders of at least a majority of the outstanding shares entitled to
vote on such removal; PROVIDED, HOWEVER, that unless the entire Board is
removed, no individual director may be removed when the votes cast against
such director's removal, or not consenting in writing to such removal, would
be sufficient to elect that director if voted cumulatively at an election
which the same total number of votes were cast (or, if such action is taken by
written consent, all shares entitled to vote were voted) and the entire number
of directors authorized at the time of such director's most recent election
were then being elected.

          2. At any time or times that the corporation is not subject to
Section 2115(b) of the CGCL and subject to any limitations imposed by law,
Section C.1. above shall no longer apply and removal shall be as provided in
Section 141(k) of the DGCL.

     D. VACANCIES.

          1. 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.

          2. 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.


                                       4.
<PAGE>

          3. At any time or times that the corporation is subject to Section
2115(b) of the CGCL, if, after the filling of any vacancy by the directors
then in office who have been elected by stockholders shall constitute less
than a majority of the directors then in office, then:

                 (a) Any holder or holders of an aggregate offive percent (5%)
or more of the total number of shares at the time outstanding having the right
to vote for those directors may call a special meeting of stockholders; or

                 (b) The Superior Court of the proper county shall, upon
application of such stockholder or stockholders, summarily order a special
meeting of stockholders, to be held to elect the entire board, all in
accordance with Section 305(c) of the CGCL. The term of office of any director
shall terminate upon that election of a successor.

     E. BYLAW AMENDMENTS. 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.

     F. BALLOTS. The directors of the corporation need not be elected by
written ballot unless the Bylaws so provide.

     G. ACTION BY STOCKHOLDERS. 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; no action shall be taken by the
stockholders by written consent.

     H.       ADVANCE NOTICE. 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.

     I.       SPECIAL MEETINGS OF STOCKHOLDERS.  Special meetings of the
stockholders may be called only by the Chairman of the Board, the Chief
Executive Officer, or a majority of the members of the Board of Directors.

                                  ARTICLE VI.

     A. NO PERSONAL 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 (1) for any
breach of the director's duty of loyalty to the corporation and its
stockholders; (2) for acts or omissions not in good faith or which involve
intentional misconduct or knowing violations of law; (3) under section 174 of
the Delaware General Corporation law, or (4) for any transaction from which
the director derived an improper personal benefit.

     B. INDEMNIFICATION. Each person who is 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
(hereinafter a "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 of the corporation or is


                                       5.
<PAGE>

or was serving at the request of the corporation as a director, 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 a 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 any 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 expense, 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 inure to the
benefit of his or her heirs, executors and administrators; provided, however,
that, except as provided in the second paragraph hereof, the corporation shall
indemnify any such person seeking indemnification in connection with a
proceeding (or part thereof) initiated by such person only if such proceeding
(or part thereof), was authorized by the Board of Directors of the
corporation. The right to indemnification conferred in this section shall be a
contract right and shall include the right to be paid by the corporation for
any expenses incurred in defending any such proceeding in advance of its final
disposition; provided, however, that, if the Delaware General Corporation Law
requires, the payment of such expenses incurred by a director or officer 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 a 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 shall ultimately be determined
that such director or officer is not entitled to be indemnified under this
section or otherwise. The corporation may, by action of its Board of
Directors, provide indemnification to employees and agents of the corporation
with the same scope and effect as the foregoing indemnification of directors
and officers.

         If a claim under the first paragraph of this section is not paid in
full by the corporation within thirty (30) 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 in 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 is required, has been tendered to the
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 indemnity the claimant for the amount claimed, but the burden of proving
such 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


                                       6.
<PAGE>

defense to the action or create a presumption that the claimant has not met
the applicable standard of conduct.

         The right to indemnification and the payment of expenses incurred in
defending a proceeding in advance of its final disposition conferred in this
section shall not be exclusive of any other right which any person may have or
hereafter acquire under any statute, provision of this Certificate of
Incorporation, by-law, agreement, vote of stockholders or disinterested
directors or otherwise.

     C. INSURANCE. The corporation may maintain insurance, at its expense, to
protect itself and any 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.

     D. REPEAL AND MODIFICATION. Any repeal or modification of the foregoing
provisions of this Article 7 shall not adversely affect any right or
protection of a director, officer, employee or agent of the corporation
existing at the time of such repeal or modification.

     E. VOTE REQUIRED TO AMEND OR REPEAL. The amendment or repeal of this
Article 7 shall require the approval of the holders of shares representing at
least sixty six and two-thirds percent (66-2/3%) of the shares of the
corporation entitled to vote in the election of directors, voting as one class.

                                  ARTICLE 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.


                                       7.
