FORM 3

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 INITIAL STATEMENT OF BENEFICIAL OWNERSHIP OF SECURITIES Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940

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(Print or Type Responses)

1. Name and Address of Reporting Person *   Fort Mason Capital, LLC 2. Date of Event Requiring Statement (Month/Day/Year) 09/27/2005 3. Issuer Name and Ticker or Trading Symbol NANOGEN INC [NGEN] (Last) (First) (Middle) 456 MONTGOMERY STREET, 22ND FLOOR 4. Relationship of Reporting Person(s) to Issuer (Check all applicable) _____ Director __X__ 10% Owner _____ Officer (give title below) _____ Other (specify below) 5. If Amendment, Date Original Filed(Month/Day/Year) (Street) SAN FRANCISCO, CA 94104 6. Individual or Joint/Group Filing(Check Applicable Line) _X_ Form filed by One Reporting Person ___ Form filed by More than One Reporting Person (City) (State) (Zip) Table I - Non-Derivative Securities Beneficially Owned

1.Title of Security (Instr. 4) 2. Amount of Securities Beneficially Owned (Instr. 4) 3. Ownership Form: Direct (D) or Indirect (I) (Instr. 5) 4. Nature of Indirect Beneficial Ownership (Instr. 5) Common Stock, par value $0.001 per share 5,102,041 (1) (2) I (1) (2) By limited partnerships (1) (2)

Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.			SEC 1473 (7-02)
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Table II - Derivative Securities Beneficially Owned (e.g., puts, calls, warrants, options, convertible securities)

1. Title of Derivative Security (Instr. 4)	2. Date Exercisable and Expiration Date (Month/Day/Year)		3. Title and Amount of Securities Underlying Derivative Security (Instr. 4)		4. Conversion or Exercise Price of Derivative Security	5. Ownership Form of Derivative Security: Direct (D) or Indirect (I) (Instr. 5)	6. Nature of Indirect Beneficial Ownership (Instr. 5)
	Date Exercisable	Expiration Date	Title	Amount or Number of Shares
Common Stock Warrants (right to buy) (1) (2)	09/28/2005	09/28/2010	Common Stock, par value $0.001 per share	765,306	$ 4	I (1) (2)	By limited partnerships (1) (2)

Reporting Owners

Reporting Owner Name / Address	Relationships
	Director	10% Owner	Officer	Other
Fort Mason Capital, LLC 456 MONTGOMERY STREET 22ND FLOOR SAN FRANCISCO, CA 94104	Â	  X	Â	Â

Signatures

/s/Dan German, Managing Member		10/12/2005
**Signature of Reporting Person		Date

Explanation of Responses:

*	If the form is filed by more than one reporting person, see Instruction 5(b)(v).
**	Intentional misstatements or omissions of facts constitute Federal Criminal Violations. See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).
(1)	Fort Mason Master, LP, a Cayman Islands limited partnership ("Master"), and Fort Mason Partners, LP, a Delaware limited partnership ("Partners" and, together with Master, the "Funds"), are the holders of, in the aggregate, 5,102,041 shares of the common stock, par value $0.001 per share (the "Shares"), of Nanogen, Inc., a Delaware corporation (the "Company"), and warrants that entitle the Funds to purchase up to an aggregate of 765,306 additional Shares. The Funds acquired such Shares and warrants in a registered direct offering of up to 6,802,721 units at $2.94 per unit, with each unit consisting of (i) one (1) Share and (ii) one (1) warrant to purchase 0.15 Shares. Fort Mason Capital, LLC, a Delaware limited liability company ("Capital"), serves as the investment manager of the Funds and possesses sole power to vote and direct the disposition of all securities of the Company held by the Funds.
(2)	Thus, as of September 27, 2005, for the purposes of Reg. Section 240.13d-3, Capital is deemed to beneficially own 5,867,347 Shares. Capital's interest in the securities reported herein is limited to the extent of its pecuniary interest in the Funds, if any.

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