SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G/A INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1 (b), (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2 (b) (Amendment No. 1)* Aerogen, Inc. -------------------------------------------------------------------------------- (Name of Issuer) Common Stock -------------------------------------------------------------------------------- (Title of Class of Securities) 007779309 -------------------------------------------------------------------------------- (CUSIP Number) December 31, 2004 -------------------------------------------------------------------------------- (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to which this Schedule is filed: [ ] Rule 13d-1(b) [ ] Rule 13d-1(c) [X] Rule 13d-1(d) *The remainder of this cover page shall be filled out for a reporting person's initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page. The information required on the remainder of this cover page shall not be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange Act of 1934 ("Act") or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes). (Continued on following pages) Page 1 of 12 Pages ---------------------------------------------------------- -------------------------------------- CUSIP NO. 007779101 13 G Page 2 of 12 Pages ---------------------------------------------------------- -------------------------------------- ------------ --------------------------------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON I.R.S. IDENTIFICATION NO. OF ABOVE PERSONS (ENTITIES ONLY) U.S. Venture Partners IV, L.P. ("USVP IV") ------------ --------------------------------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) [ ] (b) [X] ------------ --------------------------------------------------------------------------------------------------------- 3 SEC USE ONLY ------------ --------------------------------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION Delaware ------------ --------------------------------------------------------------------------------------------------------- NUMBER OF SHARES 5 SOLE VOTING POWER BENEFICIALLY 307,959 shares, except that Presidio Management Group IV, L.P. OWNED BY EACH ("PMG IV"), the general partner of USVP IV, may be deemed to have sole REPORTING voting power with respect to such shares, and William K Bowes, Jr. PERSON ("Bowes"), Irwin Federman ("Federman"), Steven M. Krausz ("Krausz") WITH and Philip M. Young ("Young"), the general partners of PMG IV, may be deemed to have shared voting power with respect to such shares. -------- ------------------------------------------------------------------------ 6 SHARED VOTING POWER See response to row 5. -------- ------------------------------------------------------------------------ 7 SOLE DISPOSITIVE POWER 307,959 shares, except that PMG IV, the general partner of USVP IV, may be deemed to have sole dispositive power with respect to such shares, and Bowes, Federman, Krausz and Young, the general partners of PMG IV, may be deemed to have shared dispositive power with respect to such shares. -------- ------------------------------------------------------------------------ 8 SHARED DISPOSITIVE POWER See response to row 7. ------------ --------------------------------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 307,959 ------------ --------------------------------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* [ ] ------------ --------------------------------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 6.3% ------------ --------------------------------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN ------------ ---------------------------------------------------------------------------------------------------------* SEE INSTRUCTIONS BEFORE FILLING OUT! ---------------------------------------------------------- -------------------------------------- CUSIP NO. 007779101 13 G Page 3 of 12 Pages ---------------------------------------------------------- -------------------------------------- ------------ --------------------------------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON I.R.S. IDENTIFICATION NO. OF ABOVE PERSONS (ENTITIES ONLY) Second Ventures II, L.P. ("SV II") ------------ --------------------------------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) [ ] (b) [X] ------------ --------------------------------------------------------------------------------------------------------- 3 SEC USE ONLY ------------ --------------------------------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION Cayman Islands ------------ --------------------------------------------------------------------------------------------------------- NUMBER OF SHARES 5 SOLE VOTING POWER BENEFICIALLY 37,386 shares, except that PMG IV, the general partner of SV II, may OWNED BY EACH be deemed to have sole voting power with respect to such shares, and REPORTING Bowes, Federman, Krausz and Young, the general partners of PMG IV, may PERSON be deemed to have shared voting power with respect to such shares. WITH -------- ------------------------------------------------------------------------ 6 SHARED VOTING POWER See response to row 5. -------- ------------------------------------------------------------------------ 7 SOLE DISPOSITIVE POWER 37,386 shares, except that PMG IV, the general partner of SV II, may be deemed to have sole dispositive power with respect to such shares, and Bowes, Federman, Krausz and Young, the general partners of PMG IV, may be deemed to have shared dispositive power with respect to such shares. -------- ------------------------------------------------------------------------ 8 SHARED DISPOSITIVE POWER See response to row 7. ------------ --------------------------------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 37,386 ------------ --------------------------------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* [ ] ------------ --------------------------------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 0.8 % ------------ --------------------------------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN ------------ ---------------------------------------------------------------------------------------------------------* SEE INSTRUCTIONS BEFORE FILLING OUT! ---------------------------------------------------------- -------------------------------------- CUSIP NO. 007779101 13 G Page 4 of 12 Pages ---------------------------------------------------------- -------------------------------------- ------------ --------------------------------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON I.R.S. IDENTIFICATION NO. OF ABOVE PERSONS (ENTITIES ONLY) USVP Entrepreneur Partners II, L.P. ("UEP II") ------------ --------------------------------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) [ ] (b) [X] ------------ --------------------------------------------------------------------------------------------------------- 3 SEC USE ONLY ------------ --------------------------------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION Delaware ------------------------------------ -------- ------------------------------------------------------------------------ NUMBER OF SHARES 5 SOLE VOTING POWER BENEFICIALLY 10,684 shares, except that PMG IV, the general partner of UEP II, may OWNED BY EACH be deemed to have sole voting power with respect to such shares, and REPORTING Bowes, Federman, Krausz and Young, the general partners of PMG IV, may PERSON be deemed to have shared voting power with respect to such shares. WITH -------- ------------------------------------------------------------------------ 6 SHARED VOTING POWER See response to row 5. -------- ------------------------------------------------------------------------ 7 SOLE DISPOSITIVE POWER 10,684 shares, except that PMG IV, the general partner of UEP II, may be deemed to have sole dispositive power with respect to such shares, and Bowes, Federman, Krausz and Young, the general partners of PMG IV, may be deemed to have shared dispositive power with respect to such shares. -------- ------------------------------------------------------------------------ 8 SHARED DISPOSITIVE POWER See response to row 7. ------------------------------------ -------- ------------------------------------------------------------------------ 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 10,684 ------------ --------------------------------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* [ ] ------------ --------------------------------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 0.2% ------------ --------------------------------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN ------------ ---------------------------------------------------------------------------------------------------------* SEE INSTRUCTIONS BEFORE FILLING OUT! ---------------------------------------------------------- -------------------------------------- CUSIP NO. 007779101 13 G Page 5 of 12 Pages ---------------------------------------------------------- -------------------------------------- ------------ --------------------------------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON I.R.S. IDENTIFICATION NO. OF ABOVE PERSONS (ENTITIES ONLY) Presidio Management Group IV, L.P. ("PMG IV") ------------ --------------------------------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) [ ] (b) [X] ------------ --------------------------------------------------------------------------------------------------------- 3 SEC USE ONLY ------------ --------------------------------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION Delaware ------------ --------------------------------------------------------------------------------------------------------- NUMBER OF SOLE VOTING POWER SHARES 5 356,029 shares, of which 307,959 are directly owned by USVP IV, 37,386 BENEFICIALLY are directly owned by SV II and 10,684 are directly owned by UEP II. OWNED BY EACH PMG IV is the general partner of USVP IV, SV II and UEP II, and may be REPORTING deemed to have sole voting power with respect to such shares, and PERSON Bowes, Federman, Krausz and Young, the general partners of PMG IV, may WITH be deemed to have shared voting power with respect to such shares. -------- ------------------------------------------------------------------------ 6 See response to row 5. -------- ------------------------------------------------------------------------ 7 SOLE DISPOSITIVE POWER 356,029 shares, of which 307,959 are directly owned by USVP IV, 37,386 are directly owned by SV II and 10,684 are directly owned by UEP II. PMG IV is the general partner of USVP IV, SV II and UEP II, and may be deemed to have sole dispositive power with respect to such shares, and Bowes, Federman, Krausz and Young, the general partners of PMG IV, may be deemed to have shared dispositive power with respect to such shares. -------- ------------------------------------------------------------------------ 8 SHARED DISPOSITIVE POWER See response to row 7. ------------------------------------ -------- ------------------------------------------------------------------------ 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 356,029 ------------ --------------------------------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* [ ] ------------ --------------------------------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 7.3% ------------ --------------------------------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN ------------ ---------------------------------------------------------------------------------------------------------* SEE INSTRUCTIONS BEFORE FILLING OUT! ---------------------------------------------------------- -------------------------------------- CUSIP NO. 007779101 13 G Page 6 of 12 Pages ---------------------------------------------------------- -------------------------------------- ------------ --------------------------------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON I.R.S. IDENTIFICATION NO. OF ABOVE PERSONS (ENTITIES ONLY) William K. Bowes, Jr. ("Bowes") ------------ --------------------------------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) [ ] (b) [X] ------------ --------------------------------------------------------------------------------------------------------- 3 SEC USE ONLY ------------ --------------------------------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION U.S. Citizen ------------ --------------------------------------------------------------------------------------------------------- NUMBER OF SHARES 5 SOLE VOTING POWER BENEFICIALLY 0 shares. OWNED BY EACH -------- ------------------------------------------------------------------------ REPORTING PERSON 6 SHARED VOTING POWER WITH 356,029 shares, of which 307,959 are directly owned by USVP IV, 37,386 are directly owned by SV II and 10,684 are directly owned by UEP II. Bowes is a general partner of PMG IV, the general partner of USVP IV, SV II and UEP II, and may be deemed to have shared voting power with respect to such shares. -------- ------------------------------------------------------------------------ 7 SOLE DISPOSITIVE POWER 0 shares. -------- ------------------------------------------------------------------------ 8 SHARED DISPOSITIVE POWER 356,029 shares, of which 307,959 are directly owned by USVP IV, 37,386 are directly owned by SV II and 10,684 are directly owned by UEP II. Bowes is a general partner of PMG IV, the general partner of USVP IV, SV II and UEP II, and may be deemed to have shared dispositive power with respect to such shares. ------------ --------------------------------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 356,029 ------------ --------------------------------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* [ ] ------------ --------------------------------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 7.3% ------------ --------------------------------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* IN ------------ ---------------------------------------------------------------------------------------------------------* SEE INSTRUCTIONS BEFORE FILLING OUT! ---------------------------------------------------------- -------------------------------------- CUSIP NO. 007779101 13 G Page 7 of 12 Pages ---------------------------------------------------------- -------------------------------------- ------------ --------------------------------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON I.R.S. IDENTIFICATION NO. OF ABOVE PERSONS (ENTITIES ONLY) Irwin Federman ("Federman") ------------ --------------------------------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) [ ] (b) [X] ------------ --------------------------------------------------------------------------------------------------------- 3 SEC USE ONLY ------------ --------------------------------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION U.S. Citizen ------------ --------------------------------------------------------------------------------------------------------- NUMBER OF SHARES 5 SOLE VOTING POWER BENEFICIALLY 0 shares. OWNED BY EACH -------- ------------------------------------------------------------------------ REPORTING PERSON 6 SHARED VOTING POWER WITH 356,029 shares, of which 307,959 are directly owned by USVP IV, 37,386 are directly owned by SV II and 10,684 are directly owned by UEP II. Federman is a general partner of PMG IV, the general partner of USVP IV, SV II and UEP II, and may be deemed to have shared voting power with respect to such shares. -------- ------------------------------------------------------------------------ 7 SOLE DISPOSITIVE POWER 0 shares. -------- ------------------------------------------------------------------------ 8 SHARED DISPOSITIVE POWER 356,029 shares, of which 307,959 are directly owned by USVP IV, 37,386 are directly owned by SV II and 10,684 are directly owned by UEP II. Federman is a general partner of PMG IV, the general partner of USVP IV, SV II and UEP II, and may be deemed to have shared dispositive power with respect to such shares. ------------------------------------ -------- ------------------------------------------------------------------------ 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 356,029 ------------ --------------------------------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* [ ] ------------ --------------------------------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 7.3% ------------ --------------------------------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* IN ------------ ---------------------------------------------------------------------------------------------------------* SEE INSTRUCTIONS BEFORE FILLING OUT! ---------------------------------------------------------- -------------------------------------- CUSIP NO. 007779101 13 G Page 8 of 12 Pages ---------------------------------------------------------- -------------------------------------- ------------ --------------------------------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON I.R.S. IDENTIFICATION NO. OF ABOVE PERSONS (ENTITIES ONLY) Steven M. Krausz ("Krausz") ------------ --------------------------------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) [ ] (b) [X] ------------ --------------------------------------------------------------------------------------------------------- 3 SEC USE ONLY ------------ --------------------------------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION U.S. Citizen ------------ --------------------------------------------------------------------------------------------------------- NUMBER OF SHARES 5 SOLE VOTING POWER BENEFICIALLY 0 shares. OWNED BY EACH -------- ------------------------------------------------------------------------ REPORTING PERSON 6 SHARED VOTING POWER WITH 356,029 shares, of which 307,959 are directly owned by USVP IV, 37,386 are directly owned by SV II and 10,684 are directly owned by UEP II. Krausz is a general partner of PMG IV, the general partner of USVP IV, SV II and UEP II, and may be deemed to have shared voting power with respect to such shares. -------- ------------------------------------------------------------------------ 7 SOLE DISPOSITIVE POWER 0 shares. -------- ------------------------------------------------------------------------ 8 SHARED DISPOSITIVE POWER 356,029 shares, of which 307,959 are directly owned by USVP IV, 37,386 are directly owned by SV II and 10,684 are directly owned by UEP II. Krausz is a general partner of PMG IV, the general partner of USVP IV, SV II and UEP II, and may be deemed to have shared dispositive power with respect to such shares. ------------------------------------ -------- ------------------------------------------------------------------------ 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 356,029 ------------ --------------------------------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* [ ] ------------ --------------------------------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 7.3% ------------ --------------------------------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* IN ------------ ---------------------------------------------------------------------------------------------------------*SEE INSTRUCTIONS BEFORE FILLING OUT! ---------------------------------------------------------- -------------------------------------- CUSIP NO. 007779101 13 G Page 9 of 12 Pages ---------------------------------------------------------- -------------------------------------- ------------ --------------------------------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON I.R.S. IDENTIFICATION NO. OF ABOVE PERSONS (ENTITIES ONLY) Philip M. Young ("Young") ------------ --------------------------------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) [ ] (b) [X] ------------ --------------------------------------------------------------------------------------------------------- 3 SEC USE ONLY ------------ --------------------------------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION U.S. Citizen ------------ --------------------------------------------------------------------------------------------------------- NUMBER OF SHARES 5 SOLE VOTING POWER BENEFICIALLY 15,194 shares. OWNED BY EACH -------- ------------------------------------------------------------------------ REPORTING PERSON 6 SHARED VOTING POWER WITH 356,029 shares, of which 307,959 are directly owned by USVP IV, 37,386 are directly owned by SV II and 10,684 are directly owned by UEP II. Young is a general partner of PMG IV, the general partner of USVP IV, SV II and UEP II, and may be deemed to have shared voting power with respect to such shares. -------- ------------------------------------------------------------------------ 7 SOLE DISPOSITIVE POWER 15,194 shares. -------- ------------------------------------------------------------------------ 8 SHARED DISPOSITIVE POWER 356,029 shares, of which 307,959 are directly owned by USVP IV, 37,386 are directly owned by SV II and 10,684 are directly owned by UEP II. Young is a general partner of PMG IV, the general partner of USVP IV, SV II and UEP II, and may be deemed to have shared dispositive power with respect to such shares. ------------------------------------ -------- ------------------------------------------------------------------------ 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 371,223 ------------ --------------------------------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* [ ] ------------ --------------------------------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 7.6% ------------ --------------------------------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* IN ------------ ---------------------------------------------------------------------------------------------------------* SEE INSTRUCTIONS BEFORE FILLING OUT! Page 10 of 12 Pages This Amendment No. 1 amends the previous statement on Schedule 13G filed by U.S. Venture Partners IV, L.P., Second Ventures II, L.P., USVP Entrepreneur Partners II, L.P., Presidio Management Group IV, L.P., William K. Bowes, Jr., Irwin Federman, Steven M. Krausz and Philip M. Young. The foregoing entities and individuals are collectively referred to as the "Reporting Persons." Only those items as to which there has been a change are included in this Amendment No. 1. ITEM 4. OWNERSHIP: The following information with respect to the ownership of the Common Stock of the issuer by the persons filing this Statement is provided as of December 31, 2004: (a) Amount beneficially owned: See Row 9 of cover page for each Reporting Person. (b) Percent of Class: See Row 11 of cover page for each Reporting Person. (c) Number of shares as to which such person has: (i) Sole power to vote or to direct the vote: See Row 5 of cover page for each Reporting Person. (ii) Shared power to vote or to direct the vote: See Row 6 of cover page for each Reporting Person. (iii) Sole power to dispose or to direct the disposition of: See Row 7 of cover page for each Reporting Person. (iv) Shared power to dispose or to direct the disposition of: See Row 8 of cover page for each Reporting Person. Page 11 of 12 Pages SIGNATURES 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. Dated: February 10, 2005 U.S. Venture Partners IV, L.P. /s/ Michael Maher By Presidio Management Group IV, L.P. -------------------------------------------------- Its General Partner Signature Michael Maher Chief Financial Officer/Attorney-In-Fact Second Ventures II, L.P. /s/ Michael Maher By Presidio Management Group IV, L.P. -------------------------------------------------- Its General Partner Signature Michael Maher Chief Financial Officer/Attorney-In-Fact USVP Entrepreneur Partners II, L.P. /s/ Michael Maher By Presidio Management Group IV, L.P. -------------------------------------------------- Its General Partner Signature Michael Maher Chief Financial Officer/Attorney-In-Fact Presidio Management Group IV, L.P. /s/ Michael Maher A Delaware Limited Partnership -------------------------------------------------- Signature Michael Maher Chief Financial Officer/Attorney-In-Fact William K. Bowes, Jr. /s/ Michael Maher -------------------------------------------------- Michael Maher Attorney-In-Fact Page 12 of 12 Pages Irwin Federman /s/ Michael Maher -------------------------------------------------- Michael Maher Attorney-In-Fact Steven M. Krausz /s/ Michael Maher -------------------------------------------------- Michael Maher Attorney-In-Fact Philip M. Young /s/ Michael Maher -------------------------------------------------- Michael Maher Attorney-In-Fact