SecProbe.io

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Mail Stop 0610

							June 13, 2005

Via Facsimile and U.S. Mail

Mr. Robert Saltmarsh
Chief Financial Officer
Nanogen, Inc.
10398 Pacific Center Court
San Diego, CA 92121

	Re:	Nanogen, Inc.
		Form 10-K for the fiscal year ended December 31, 2004
		Form 10-Q for the quarterly period ended March 31, 2005
		File No. 000-23541

Dear Mr. Saltmarsh:

      We have reviewed your response letter dated May 17, 2005 and
have the following additional comments.  We have limited our
review
to matters related to the issues raised in our comments.  Where
indicated, we think you should revise your future filings in
response
to these comments.  If you disagree, we will consider your
explanation as to why our comment is inapplicable or a revision is
unnecessary.  Please be as detailed as necessary in your
explanation.
In some of our comments, we may ask you to provide us with
supplemental information so we may better understand your
disclosure.
After reviewing this information, we may or may not raise
additional
comments.

      Please understand that the purpose of our review process is
to
assist you in your compliance with the applicable disclosure
requirements and to enhance the overall disclosure in your filing.
We look forward to working with you in these respects.  We welcome
any questions you may have about our comment or on any other
aspects
of our review.  Feel free to call us at the telephone numbers
listed
at the end of this letter.

Form 10-Q for the Quarterly Period Ended March 31, 2005

Item 4.  Controls and Procedures, page 39

1. In future filings, please omit the "in providing reasonable
assurance that" language that currently appears after the word
"effective" in your Item 4a disclosures.  While you may, if
desired,
state that your disclosure controls and procedures are effective
"at
the reasonable assurance level," we do not believe that the "in
providing reasonable assurance that" language is consistent with
the
definition of disclosure controls and procedures set forth in Rule
13a-15(e) of the Exchange Act.

2. We note your statement that a "control system, no matter how
well
conceived and operated, can provide only reasonable assurance of
achieving the desired control objectives."  Please revise future
filings to state clearly, if true, that your disclosure controls
and
procedures are designed to provide reasonable assurance of
achieving
their objectives and that your principal executive officer and
principal financial officer concluded that your disclosure
controls
and procedures are effective at that reasonable assurance level.
In
the alternative, remove the reference to the level of assurance of
your disclosure controls and procedures.  Please refer to Section
II.F.4 of Management`s Reports on Internal Control Over Financial
Reporting and Certification of Disclosure in Exchange Act Periodic
Reports, SEC Release No. 33-8238, available on our website at
<http://www.sec.gov/rules/final/33-8238.htm>.

* * * * * * * *
      As appropriate, please respond to these comments within 10
business days or tell us when you will provide us with a response.
Please furnish a cover letter with your response that keys your
responses to our comments and provides any requested supplemental
information.  Detailed cover letters greatly facilitate our
review.
Please file your cover letter on EDGAR.  Please understand that we
may have additional comments after reviewing your amendment and
responses to our comments.

	You may contact Eric Atallah, Staff Accountant at (202) 551-
3663
or me at (202) 551-3603 regarding comments on the financial
statements and related matters.  In this regard, do not hesitate
to
contact Angela Crane, Branch Chief, at (202) 551-3554.

      								  Sincerely,

								  Jay Webb
								  Reviewing Accountant
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Mr. Robert Saltmarsh
Nanogen, Inc.
June 13, 2005
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