Company Name: Nanogen, Inc.
Public Availability Date: April 18, 2006

Document Sections:

INQUIRY LETTER
APPENDIX
STAFF REPLY LETTER

[INQUIRY LETTER]

William L. Respess

Sr. Vice President, General Counsel

VIA FEDERAL EXPRESS

March 23, 2006

U.S. Securities and Exchange Commission
Division of Corporation Finance
Office of the Chief Counsel
100 F Street, N.E.
Washington, D.C. 20549

Re: Securities Exchange Act of 1934/Rule 14a-8(e)(2) No Action Request for Exclusion of Stockholder Proposal

Ladies and Gentlemen:

This letter requests your concurrence with the conclusion of Nanogen, Inc., a Delaware corporation ("Nanogen"), that it can exclude from its proxy statement and form of proxy for its 2006 Annual Meeting of Stockholders ("2006 Proxy Materials") a stockholder proposal (the "Proposal") that it received via email from Peter Buchta on February 24, 2006. Mr. Buchta's email and the Proposal are attached to this letter as Exhibit A.

Nanogen believes that it may properly exclude the Proposal from its 2006 Proxy Materials because Mr. Buchta failed to submit the Proposal in a timely manner pursuant to Rule 14a-8(e)(2) of the Securities Exchange Act of 1934, as amended (the "Exchange Act"). Nanogen's proxy statement released to stockholders for its 2005 annual meeting of stockholders was dated April 29, 2005. Accordingly, pursuant to Rule 14a-8(e)(2), December 31, 2005 was the latest date for a stockholder to submit a proposal for inclusion in Nanogen's 2006 Proxy Materials. This submission deadline is clearly stated on page 35 of Nanogen's 2005 proxy statement. Nanogen received the Proposal on February 24, 2006 via email. Therefore, Nanogen intends to exclude the Proposal from its 2006 Proxy Materials pursuant to Rule 14a-8(e)(2).

Rule 14a-8(j) provides that a company must file its Rule 14a-8 no action request no later than 80 calendar days before it files its definitive proxy statement and form of proxy with the Securities and Exchange Commission (the "Commission"). The Commission staff may permit the company to make its submission later than 80 days before the company files its definitive proxy statement and form of proxy if the company demonstrates "good cause" for missing the deadline line. The Commission staff has stated that the most common basis of the company's showing of good cause is that the proposal was not submitted timely and the company did not receive the Proposal until after the 80-day deadline had passed. See Staff Legal Bulletin No. 14B (CF) (avail. Sept. 15, 2004). As of today's date, Nanogen anticipates filing its definitive proxy statement for its 2006 Annual Meeting of Stockholders on or about April 29, 2006. Nanogen did not receive the Proposal until February 24, 2006, or after 80-day deadline had passed. Therefore, Nanogen respectfully requests that the staff waive the 80-day deadline on the basis of a showing of good cause under Rule 14a-8(j).

For the foregoing reasons, we respectfully request that the Staff of the Division of Corporation Finance concur that Nanogen may properly exclude the Proposal from its 2006 Proxy Materials and that it will not recommend any enforcement action to the Commission if Nanogen excludes the Proposal from its 2006 Proxy Materials. In addition, Nanogen requests that the Staff waive the 80-day requirement on the basis of a showing of good cause under Rule 14a-8(j) because Nanogen did not receive the Proposal until after the 80-day deadline had passed.

Enclosed pursuant to Rule 14a-8(j) of the Exchange Act are six copies of this letter and its attachments. Also, in accordance with Rule 14a-8(j), a copy of this letter and its attachments are being mailed on this date to Mr. Buchta informing him of our intention to exclude the Proposal from the 2006 Proxy Materials.

If you have any questions or require additional information concerning this request, please call me at 858.410.4702 or Scott Karchmer at Morgan, Lewis & Bockius LLP at 415.442.1091. If possible, I would appreciate it if the Staff would send a copy of their response to this request to me by fax at 858.410.4949 when it is available.

Sincerely,

/s/

William L. Respess
Senior Vice President, General Counsel and Secretary

Enclosures

cc: Peter Buchta
35 Oswald Place
Staten Island, NY 10309

Scott D. Karchmer
Morgan, Lewis & Bockius LLP

[APPENDIX]
From: Respess, Larry

Sent: Thursday, March 23, 2006 12:24 PM

To: Reeves, Debbrah

Subject: FW: Proposals for next shareholder meeting.

Original Message

From: Ludvigson, David

Sent: Friday, February 24, 2006 8:15 AM

To: Respess, Larry; skarchmer@morganlewis.com

Subject: FW: Proposals for next shareholder meeting.

I assume this person is a shareholder and would like to make some shareholder proposals. Who and how should we respond?

David

Original Message

From: Peter Buchta [mailto:pbuchtal@earthlink.net]

Sent: Friday, February 24, 2006 6:51 AM

To: Ludvigson, David

Subject: Proposals for next shareholder meeting.

David:

Below are proposals that I wish made known to management at the next shareholders meeting. Please forward information on who I should address these too.

Best,

Peter.

Peter Buchta
35 Oswald Place
Staten Island, NY 10309

Following proposals:

Shareholder's proposal to terminate all incentive programs for management and employees.

1. Termination of all incentive programs including stock options, warrants, etc. This will in effect terminate all existing options programs with all Nanogen management and employees. This includes all programs currently proposed, or in operation.

Shareholder's proposal to limit managerial salaries

1. Upper managerial salaries from VP on up shall be tied to company performance and dividends paid to investors from company's profits.

2. Salaries of current CEO, CFO, and chairman of BOD shall be frozen and tied to company performance as stated in 1.

Shareholder's proposal to limit terms of service by Chairman of Board of Directors

1. Terms of service shall be construed to the following terms listed below.

2. The BOD shall have no voting over ride in the matter. Terms of service shall be applicable for all Chairmen.

3. The normal term of service for the Chairman's position shall be 2 years.

4. The normal limits on terms of service shall be 2 consecutive terms.

5. The only exceptions to the rules are as follows:

a. Chairman holds more than 5% vested in stock or, b. Company has shown a profit for the time that the Chairperson has been in office and c. Company has paid dividends to their shareholders during the Chairperson's tenure.

[STAFF REPLY LETTER]

April 18, 2006

Response of the Office of Chief Counsel Division of Corporation Finance

Re: Nanogen, Inc.

Incoming letter dated March 23, 2006

The proposal relates to compensation and the chairman of the board.

There appears to be some basis for your view that Nanogen may exclude the proposal under rule 14a-8(e)(2) because Nanogen received it after the deadline for submitting proposals. We note your representation that Nanogen received the proposal after this deadline. Accordingly, we will not recommend enforcement action to the Commission if Nanogen omits the proposal from its proxy materials in reliance on rule 14a-8(e)(2).

We note that Nanogen did not file its statement of objections to including the proposal in its proxy materials at least 80 days before the date on which it will file definitive proxy materials as required by rule 14a-8(j)(1). Noting the circumstances of the delay, we grant Nanogen's request that the 80-day requirement be waived.

Sincerely,

/s/

Mark F. Vilardo
Special Counsel