SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                  SCHEDULE 13D
                    Under the Securities Exchange Act of 1934
--------------------------------------------------------------------------------

                                  Aerogen Corp.
                                  -------------
                                (Name of Issuer)

                                  Common Stock
                         (Title of Class of Securities)

                                    007779309
                                    ---------
                                 (CUSIP Number)

                                 Samuel D. Isaly
                              OrbiMed Advisors LLC
                               OrbiMed Capital LLC
                                767 Third Avenue
                               New York, NY 10017
                            Telephone: (212) 739-6400
                            -------------------------
                     (Name, Address and Telephone Number of
                    Person Authorized to Receive Notices and
                                 Communications)

                                    Copy to:

                             Paul S. Schreiber, Esq.
                             Shearman & Sterling LLP
                              599 Lexington Avenue
                            New York, New York 10022
                            Telephone: (212) 848-4000

                                 March 11, 2004
                                 --------------
             (Date of Event which Requires Filing of this Statement)


If the filing person has previously filed a statement on Schedule 13G to report
the acquisition which is the subject of this Schedule 13D, and is filing this
schedule because of Rule 13d-1(e), 13d-1(f), or 13d-1(g), check the following
box |_|.

Check the following box if a fee is being paid with this Statement |_|.



                                  Page 1 of 14




CUSIP No. 068750V102

(1)      Name of Reporting Person
         S.S. or I.R.S. Identification No. of Above Person

         Samuel D. Isaly
         -----------------------------------------------------------------------

(2)      Check the Appropriate Box if a Member of a Group (See Instructions)

|_|      (a)
              ------------------------------------------------------------------

|_|      (b)
              ------------------------------------------------------------------

(3)      SEC Use Only

(4)      Source of Funds (See Instructions)  AF
                                            ------------------------------------

(5)      Check if Disclosure of Legal Proceedings is Required Pursuant to Item
         2(d) or 2(e).

|_|      -----------------------------------------------------------------------

(6)      Citizenship or Place of Organization   United States
                                              ---------------------------------=

  Number of             (7)   Sole Voting Power --------------------------------
   Shares
 Beneficially           (8)   Shared Voting Power   4,000,000
  Owned by                                        ------------------------------
    Each                (9)   Sole Dispositive Power
  Reporting                                          ---------------------------
 Person With           (10)   Shared Dispositive Power   4,000,000
                                                       -------------------------

(11)     Aggregate Amount Beneficially Owned by Each Reporting Person  4,000,000
                                                                      ----------
(12)     Check if the Aggregate Amount in Row (11) Excludes Certain Shares
 |_|     (See Instructions)

         -----------------------------------------------------------------------
(13)     Percent of Class Represented by Amount in Row (11)   47.64%
                                                            --------------------
(14)     Type of Reporting Person (See Instructions)  IN
                                                     ---------------------------


                                  Page 2 of 14


CUSIP No. 068750V102

(1)      Name of Reporting Person
         S.S. or I.R.S. Identification No. of Above Person

         OrbiMed Advisors LLC
         -----------------------------------------------------------------------

(2)      Check the Appropriate Box if a Member of a Group (See Instructions)

|_|      (a)
            --------------------------------------------------------------------
|_|      (b)
            --------------------------------------------------------------------

(3)      SEC Use Only
                      ----------------------------------------------------------

(4)      Source of Funds (See Instructions) AF
                                           -------------------------------------
(5)      Check if Disclosure of Legal Proceedings is Required Pursuant to Item
         2(d) or 2(e).
|_|      -----------------------------------------------------------------------

(6)      Citizenship or Place of Organization   Delaware
                                              ----------------------------------
  Number of        (7)  Sole Voting Power
   Shares                                  -------------------------------------
 Beneficially      (8)  Shared Voting Power    2,550,000
  Owned by                                  ------------------------------------
    Each           (9)  Sole Dispositive Power
 Reporting                                     ---------------------------------
Person With       (10)   Shared Dispositive Power   2,550,000
                                                  ------------------------------
(11)     Aggregate Amount Beneficially Owned by Each Reporting Person  2,550,000
                                                                      ----------
(12)     Check if the Aggregate Amount in Row (11) Excludes Certain Shares
         (See Instructions)
 |_|     -----------------------------------------------------------------------

(13)     Percent of Class Represented by Amount in Row (11)    30.4%
                                                            --------------------
(14)     Type of Reporting Person (See Instructions)  IA
                                                     ---------------------------


                                  Page 3 of 14




(1)      Name of Reporting Person
         S.S. or I.R.S. Identification No. of Above Person

         OrbiMed Capital LLC
         -----------------------------------------------------------------------

(2)      Check the Appropriate Box if a Member of a Group (See Instructions)

|_|      (a)
             -------------------------------------------------------------------
|_|      (b)
             -------------------------------------------------------------------

(3)      SEC Use Only
                      ----------------------------------------------------------
(4)      Source of Funds (See Instructions)  AF
                                            ------------------------------------
(5)      Check if Disclosure of Legal Proceedings is Required Pursuant to Item
         2(d) or 2(e).
|_|      ----------------------------------------------------------------------

(6) Citizenship or Place of Organization   Delaware
                                         --------------------------------------


 Number of              (7)    Sole Voting Power
   Shares                                         ------------------------------
Beneficially            (8)    Shared Voting Power    1,450,000
  Owned by                                         -----------------------------
    Each                (9)    Sole Dispositive Power
  Reporting                                            -------------------------
 Person With           (10)    Shared Dispositive Power    1,450,000
                                                        ------------------------
(11)     Aggregate Amount Beneficially Owned by Each Reporting Person  1,450,000
                                                                      ----------
(12)     Check if the Aggregate Amount in Row (11) Excludes Certain Shares
         (See Instructions)
|_|      -----------------------------------------------------------------------

(13)     Percent of Class Represented by Amount in Row (11)   17.3%
                                                            --------------------
(14)     Type of Reporting Person (See Instructions)  CO
                                                     ---------------------------

                                  Page 4 of 14


Item 1.  Security and Issuer.
         -------------------

         The class of equity securities to which this Statement on Schedule 13D
relates is the Preferred Stock (the "Shares"), of Aerogen Corp. (the "Issuer"),
with its principal executive offices located at 2071 Stierlin Court, Mountain
View, CA, 94043.

Item 2.  Identity and Background.
         ----------------------

         (a) This statement is being filed by Samuel D. Isaly, an individual
("Isaly"), and by OrbiMed Advisors LLC and OrbiMed Capital LLC, limited
liability companies organized under the laws of Delaware.

         (b)-(c) OrbiMed Advisors LLC is a registered investment adviser under
the Investment Advisers Act of 1940, as amended that acts as investment adviser
or general partner to certain clients which hold Shares of the Issuer, as more
particularly described in Item 6 below. OrbiMed Advisors LLC has its principal
offices at 767 Third Avenue, 30th Floor, New York, NY 10017.

         OrbiMed Capital LLC is a registered investment advisor under the
Investment Advisers Act of 1940, as amended that acts as investment adviser or
general partner to certain limited partnerships as more particularly described
in Item 6 below. OrbiMed Capital LLC has its principal offices at 767 Third
Avenue, 30th Floor, New York, NY 10017.

         Isaly, a natural person, owns a controlling interest in OrbiMed
Advisors LLC and OrbiMed Capital LLC.

         The directors and executive officers of OrbiMed Advisors LLC and
OrbiMed Capital LLC are set forth on Schedules I and II, attached hereto.
Schedules I and II set forth the following information with respect to each such
person:

         (i)   name;

         (ii)  business address (or residence address where indicated);

         (iii) present principal occupation or employment and the name,
      principal business and address of any corporation or other organization in
      which such employment is conducted; and

         (iv)  citizenship.

         (d)-(e) During the last five years, neither the Reporting Persons nor
any Person named in Schedules I through IV have been (i) convicted in a criminal
proceeding (excluding traffic violations or similar misdemeanors) or (ii) a
party to a civil proceeding of a judicial or administrative body of competent
jurisdiction and as a result of such proceeding was or is subject to a judgment,
decree or final order enjoining future violations of, or prohibiting or
mandating activities subject to, federal or state securities laws or finding any
violation with respect to such laws.



                                  Page 5 of 14


         (f) Isaly is a citizen of the United States.

Item 3.  Source and Amount of Funds or Other Consideration.
         -------------------------------------------------

         On March 11, 2004, pursuant to the authority of OrbiMed Advisors LLC
and OrbiMed Capital LLC under their respective investment advisory contracts and
limited partnership or limited liability company agreements with or relating to
Caduceus Capital Trust, Caduceus Capital II, L.P., UBS Eucaplyptus Fund, Ltd.,
PaineWebber Eucalyptus Fund, Ltd., HFR SHC Aggressive Fund and Finsbury
Worldwide Pharmaceutical Trust (the "Funds") as more particularly referred to in
Item 6 below caused these clients to enter into a Series A-1 Convertible
Preferred Stock and Warrant Purchase Agreement (the "Agreement") to purchase
200,000 shares of a new class of the Issuer's preferred stock to be designated
as "Series A 6% Adjustable Cumulative Convertible Voting Preferred Stock" (the
"Preferred Stock", convertible to 2,000,000 shares of common stock) and warrants
to purchase 2,000,000 shares of common stock (the "Warrants" and together with
the Preferred Stock, the "Preferred Stock and Warrants"). The Agreement
contemplated two closings, both of which occurred on March 11, 2004 (the
"Closings"). Thereafter, as a result of their common control and mutual
affiliation, the Reporting Persons were the beneficial owners of approximately
47.64% of the outstanding Shares of the Issuer.

         None of the Reporting Persons have acquired or disposed of any
additional Shares of the Issuer since the Closings.

Item 4.  Purpose of Transaction.
         ----------------------

         As described more fully in Item 3 above, this statement relates to the
acquisition of Shares by the Reporting Persons. The Shares acquired by the
Reporting Persons have been acquired for the purpose of making an investment in
the Issuer and not with the present intention of acquiring control of the
Issuer's business on behalf of their respective advisory clients.

         The Reporting Persons from time to time intend to review their
investment in the Issuer on the basis of various factors, including the Issuer's
business, financial condition, results of operations and prospects, general
economic and industry conditions, the securities markets in general and those
for the Issuer's Shares in particular, as well as other developments and other
investment opportunities. Based upon such review, the Reporting Persons will
take such actions in the future as the Reporting Persons may deem appropriate in
light of the circumstances existing from time to time. If the Reporting Persons
believe that further investment in the Issuer is attractive, whether because of
the market price of the Issuer's Shares or otherwise, they may acquire shares of
common stock or other securities of the Issuer either in the open market or in
privately negotiated transactions. Similarly, depending on market and other
factors, the Reporting Persons may determine to dispose of some or all of the
Shares currently owned by the Reporting Persons or otherwise acquired by the
Reporting Persons either in the open market or in privately negotiated
transactions.

         Except as set forth above, the Reporting Persons have not formulated
any plans or proposals which relate to or would result in: (a) the acquisition
by any person of additional securities of the Issuer or the disposition of
securities of the Issuer, (b) an extraordinary corporate



                                  Page 6 of 14


transaction involving the Issuer or any of its subsidiaries, (c) a sale or
transfer of a material amount of the assets of the Issuer or any of its
subsidiaries, (d) any change in the present board of directors or management of
the Issuer, (e) any material change in the Issuer's capitalization or dividend
policy, (f) any other material change in the Issuer's business or corporate
structure, (g) any change in the Issuer's charter or bylaws or other or
instrument corresponding thereto or other action which may impede the
acquisition of control of the Issuer by any person, (h) causing a class of the
Issuer's securities to be deregistered or delisted, (i) a class of equity
securities of the Issuer becoming eligible for termination of registration or
(j) any action similar to any of those enumerated above.

Item 5.  Interest in Securities of the Issuer.
         ------------------------------------

         (a)-(b) As of this date of this filing, Samuel D. Isaly, OrbiMed
Advisors LLC and OrbiMed Capital LLC may be deemed directly or indirectly,
including by reason of their mutual affiliation, to be the beneficial owners of
the Preferred Stock and Warrants described in Item 3. Based upon information
contained in the most recent available filing by the Issuer with the SEC, such
Shares constitute approximately 47.64% of the issued and outstanding Shares. As
described above in Item 2, Isaly owns, pursuant to the terms of the limited
liability company agreement of each of OrbiMed Advisors LLC and OrbiMed Capital
LLC, a controlling interest in the outstanding limited liability company
interests of such entity. As a result, Samuel D. Isaly, OrbiMed Advisors LLC and
OrbiMed Capital LLC share power to direct the vote and to direct the disposition
of the Preferred Stock and Warrants described in Item 3.

         (c) Except as disclosed in Item 3, the Reporting Persons have not
effected any transaction in the Shares during the past 60 days.

         (d) Not applicable.

         (e) Not applicable.

Item 6.  Contracts, Arrangements, Understandings or Relationships with Respect
         to Securities of the Issuer.
         -----------------------------------------------------------------------

         In addition to the relationships between the Reporting Persons
described in Item 5, OrbiMed Capital LLC is the investment adviser for Finsbury
Worldwide Pharmaceutical Trust ("Finsbury Worldwide"), an investment company
incorporated in the United Kingdom, and HFR SHC Aggressive Fund ("HFR SHC
Aggressive"), a Bermuda Trust, pursuant to the terms of the investment advisory
agreement of each. OrbiMed Advisors LLC is the investment adviser for Winchester
Global Trust Company, a Bermuda Trust Limited, which acts as trustee for
Caduceus Capital Trust ("Caduceus Capital"). OrbiMed Advisors LLC is also the
general partner of Caduceus Capital II, L.P. ("Caduceus Capital II"), a Delaware
limited partnership, pursuant to the terms of its limited partnership agreement;
the JV partner of UBS Eucalyptus Fund, LLC ("UBS Eucalyptus"), a registered
investment company incorporated in Delaware, pursuant to the terms of its
limited liability company agreement; and the JV partner of PaineWebber
Eucalyptus Fund, Ltd. ("PaineWebber Eucalyptus"), an investment company
incorporated in the Cayman Islands, pursuant to the terms of its governing
documents. Pursuant to these agreements and relationships, OrbiMed Advisors LLC
and OrbiMed Capital LLC have discretionary investment management



                                  Page 7 of 14


authority with respect to the assets of Caduceus Capital, Caduceus Capital II,
UBS Eucalyptus, PaineWebber Eucalyptus, HFR SHC Aggressive and Finsbury
Worldwide. Such authority includes the power to vote and otherwise dispose of
securities purchased by Caduceus Capital, Caduceus Capital II, UBS Eucalyptus,
PaineWebber Eucalyptus, HFR SHC Aggressive and Finsbury Worldwide, including the
total Preferred Stock and Warrants of the Issuer held by Caduceus Capital,
Caduceus Capital II, UBS Eucalyptus, PaineWebber Eucalyptus, HFR SHC Aggressive
and Finsbury Worldwide, as described in Item 3. The number of the outstanding
Shares of the Issuer attributable to each of these is 1,000,000, 430,000,
1,000,000, 120,000, 140,000 and 1,300,000, respectively.

         Other than the agreements and the relationships mentioned above, to the
best knowledge of the Reporting Persons, there are no contracts, arrangements,
understandings or relationships (legal or otherwise) among the persons named in
Item 2 and between such persons and any persons with respect to any securities
of the Issuer, including, but not limited to, transfer or voting of any of the
Shares, finder's fees, joint ventures, loan or option arrangements, puts or
calls, guarantees of profits, division of profits or loss, or the giving of
withholding of proxies.




                                  Page 8 of 14




Item 7.  Material to Be Filed as Exhibits.
         --------------------------------

Exhibit                             Description
-------                             -----------

   A.    Joint Filing Agreement among Samuel D. Isaly, OrbiMed Advisors LLC and
         OrbiMed Capital LLC.




                                  Page 9 of 14




Signature



         After reasonable inquiry and to the best of my knowledge and belief, I
certify that the information set forth in this Statement is true, complete and
correct.

April 15, 2004                      SAMUEL D. ISALY


                                             By: /s/Samuel D. Isaly
                                                 -------------------------------
                                                 Name:  Samuel D. Isaly


                                             ORBIMED ADVISORS LLC


                                             By: /s/Samuel D. Isaly
                                                 -------------------------------
                                                 Name:  Samuel D. Isaly
                                                 Title:  Managing Member



                                             ORBIMED CAPITAL LLC


                                             By: /s/Samuel D. Isaly
                                                 -------------------------------
                                                 Name:  Samuel D. Isaly
                                                 Title:  Managing Member



                                 Page 10 of 14



                                   Schedule I

         The name and present principal occupation of each of the executive
officers and directors of OrbiMed Advisors LLC are set forth below. Unless
otherwise noted, each of these persons are United States citizens and have as
their business address 767 Third Avenue, New York, NY 10017.



========================================================================================================
                                    Position with Reporting
                    Name                      Person                         Principal Occupation
--------------------------------------------------------------------------------------------------------
                                                                 
Samuel D. Isaly                   Managing Partner                     Partner
                                                                       OrbiMed Advisors LLC
--------------------------------------------------------------------------------------------------------
Michael Sheffery                  Partner                              Partner
                                                                       OrbiMed Advisors LLC
--------------------------------------------------------------------------------------------------------
Carl L. Gordon                    Partner                              Partner
                                                                       OrbiMed Advisors LLC
--------------------------------------------------------------------------------------------------------
Sven Borho                        Partner                              Partner
     German and Swedish Citizen                                        OrbiMed Advisors LLC
--------------------------------------------------------------------------------------------------------
Eric A. Bittelman                 Chief Financial Officer              Chief Financial Officer
                                                                       OrbiMed Advisors LLC
========================================================================================================





                                 Page 11 of 14




                                   Schedule II


         The name and present principal occupation of each of the executive
officers and directors of OrbiMed Capital LLC are set forth below. Unless
otherwise noted, each of these persons are United States citizens and have as
their business address 767 Third Avenue, New York, NY 10017.



===============================================================================================
                                    Position with Reporting
            Name                         Person                 Principal Occupation
-----------------------------------------------------------------------------------------------
                                                        
Samuel D. Isaly                   Managing Partner            Partner
                                                              OrbiMed Capital LLC
-----------------------------------------------------------------------------------------------
Michael Sheffery                  Partner                     Partner
                                                              OrbiMed Capital LLC
-----------------------------------------------------------------------------------------------
Carl L. Gordon                    Partner                     Partner
                                                              OrbiMed Capital LLC
-----------------------------------------------------------------------------------------------
Sven Borho                        Partner                     Partner
     German and Swedish Citizen                               OrbiMed Capital LLC
-----------------------------------------------------------------------------------------------
Eric A. Bittelman                 Chief Financial Officer     Chief Financial Officer
                                                              OrbiMed Capital LLC
===============================================================================================






                                 Page 12 of 14




                                  EXHIBIT INDEX


 Exhibit                          Description                        Page No.
 -------                          -----------                        --------
    A.     Joint Filing Agreement among Samuel D. Isaly,                A-1
           OrbiMed A-1 Advisors LLC and OrbiMed Capital, LLC.





                                 Page 13 of 14




CUSIP No. 068750V102                                                   Exhibit A
                                                                       ---------

                             JOINT FILING AGREEMENT

         The undersigned hereby agree that the Statement on Schedule 13D, dated
March 11, 2004, (the "Schedule 13D"), with respect to the Common Stock, $0.001
par value per share, of Aerogen Corp. is, and any amendments thereto executed by
each of us shall be, filed on behalf of each of us pursuant to and in accordance
with the provisions of Rule 13d-1(f) under the Securities and Exchange Act of
1934, as amended, and that this Agreement shall be included as an Exhibit to the
Schedule 13D and each such amendment. Each of the undersigned agrees to be
responsible for the timely filing of the Schedule 13D and any amendments
thereto, and for the completeness and accuracy of the information concerning
itself contained therein. This Agreement may be executed in any number of
counterparts, all of which taken together shall constitute one and the same
instrument.

         IN WITNESS WHEREOF, the undersigned have executed this Agreement as of
the 15th day of April, 2004.

SAMUEL D. ISALY                                     ORBIMED ADVISORS LLC


/s/ Samuel D. Isaly                                 /s/ Samuel D. Isaly
---------------------------                         ----------------------------
                                                    Name:   Samuel D. Isaly
                                                    Title:  President


ORBIMED CAPITAL LLC



/s/ Samuel D. Isaly
---------------------------
Name:  Samuel D. Isaly
Title:  President




                                 Page 14 of 14