Exhibit 10.19

AMENDMENT NO. 2 TO SECURED CONVERTIBLE DEBENTURE AND CONSENT

THIS AMENDMENT NO. 2 TO SECURED CONVERTIBLE DEBENTURE AND CONSENT (the “Amendment”) is made as of January 20, 2004, by and between AEROGEN, INC., a Delaware corporation (the “Borrower”) and SF CAPITAL PARTNERS, LTD., or its registered assigns (the “Holder”).  Capitalized terms not otherwise defined herein shall have the meanings ascribed to them in the Debenture and Purchase Agreement (each as defined below);

WHEREAS, the Borrower issued Secured Convertible Debentures dated September 9, 2003 and amended January 7, 2004 (the “First Debenture”) and November 3, 2003 (together with the First Debenture, the “Debentures”) to the Holder, and warrants dated September 9, 2003 and November 3, 2003 (the “Warrants”) pursuant to that certain Loan and Securities Purchase Agreement, dated as of September 9, 2003, as amended by that certain Amendment dated January 7, 2004, executed by and between the Borrower and the Holder (as so amended, the “Purchase Agreement”);

WHEREAS, the Borrower is in the process of obtaining bridge financing in an aggregate principal amount of $500,000 (“Bridge Financing”) on the terms and conditions set forth in that certain term sheet by and among the Borrower and the Lender named therein (the “Bridge Lender”), and attached as Exhibit A hereto (the “Bridge Term Sheet”);

WHEREAS, in order to effect the Bridge Financing, the Borrower has requested that the Holder consent to: (1) the Borrower’s incurrence of the Indebtedness resulting from the Bridge Financing; (2) the Borrower’s grant of a Security Interest in the Collateral to secure the Borrower’s obligations to the Bridge Lender (the “Bridge Security Interest”); and (3) extend the maturity date of the Debenture to March 1, 2004, and the Holder is willing to so consent, based on the representations, and subject to the terms and conditions, set forth in this Amendment;

NOW, THEREFORE, for good and valuable consideration, and intending to be legally bound, each of the Borrower and the Holder agree as follows:

1.             Consent.

1.1          The Holder hereby consents to the Borrower’s incurrence of the Indebtedness resulting from the Bridge Financing in accordance with the terms set forth in the Bridge Term Sheet.  Borrower acknowledges that if it issues Common Stock or Common Stock Equivalents in the Bridge Financing with an Effective Price less than Holder’s relevant Conversion Price or Exercise Price, it shall result in an adjustment to the Holder’s applicable Conversion Price and Exercise Price as provided in Section 12(c) of the Debentures and Section 9(c) of the Warrants.

1.2          The Holder hereby consents to the Borrower’s grant of the Bridge Security Interest in accordance with the terms set forth in the Bridge Term Sheet.  The Holder hereby acknowledges and confirms that, irrespective of the order, time, or method of the creation, attachment, or perfection of any Liens on the Collateral by the Holder or the Bridge Lender, the Liens in the Collateral to be granted by the Borrower in favor of the Bridge Lender pursuant to the Bridge Financing documents shall under all circumstances be pari passu with the Liens granted by the Borrower to the Holder pursuant to the Security Agreements.  Actions with respect to any Collateral shall be controlled by the holder of a majority in interest of all Indebtedness owed by the Company to Holder under the Debentures and to Bridge Lender from the Bridge Financing, and any proceeds from the foreclosure and sale of Collateral shall be divided between Holder and Bridge Lender on a pro rata basis.

Notwithstanding anything to the contrary in the Purchase Agreement or any other Transaction Document, the Holder hereby acknowledges and confirms that neither the Borrower’s incurrence of the Indebtedness resulting from the Bridge Financing nor the Borrower’s grant of the Bridge Security Interest in favor of the Bridge Lender shall result in an Event of Default (as defined in the Debentures) under the Purchase Agreement, the Debentures or any other Transaction Document.

2.             Amendment.  The Debentures and Purchase Agreement are amended as follows:

2.1          The Maturity Date of the First Debenture is amended from January 15, 2004 to March 1, 2004.

2.2          The reference to January 15, 2004 in the definition of Debenture in Section 1.1 of the Purchase Agreement, as amended, shall now be March 1, 2004.

3.             Waiver.  Holder waives any default or breach by Borrower of the Debentures, Purchase Agreement or related agreements for failure to repay the Debentures prior to this Amendment.

4.             Interest.  Interest on the Debentures will continue to accrue through March 1, 2004.

5.             Termination.  This Amendment will be null and void if the Bridge Financing has not closed on the terms and conditions set forth in the Bridge Term Sheet by January 26, 2004.

6.             Counterpart.  This Amendment may be executed in two or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument.

IN WITNESS WHEREOF, the parties hereto have executed this AMENDMENT as of the date set forth in the first paragraph hereof.

EXHIBIT A

BRIDGE TERM SHEET

SUMMARY OF PROPOSED TERMS

Except for the above provisions entitled “Short Sales” and “Confidentiality,” which is expressly agreed by the Investor and the Company to be binding upon execution of this Summary of Proposed Terms, this Summary of Proposed Terms is not intended as a legally binding commitment by the Company or the Investor.

IN WITNESS WHEREOF, the undersigned have caused this Summary of Proposed Terms to be executed as of the date written below.

Dated:  January       , 2004