SecProbe.io

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Mail Stop 03-06

May 2, 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, 2005
		File No. 000-23541

Dear Mr. Saltmarsh:

      We have reviewed your filing and have the following
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-K for the fiscal year ended December 31, 2004

Item 7 - Management`s Discussion and Analysis of Financial
Condition
and Results of Operations - Page 33

Results of Operations - Page 38

Years ended December 31, 2004, 2003 and 2002 - Page 38

1. We note your discussion on page 30 of the License and Supply
Agreement with Applied Biosystems that you acquired in connection
with your acquisition of Epoch Biosciences, Inc.  It would appear
that this is a significant agreement to you.  In future filings
please make more specific disclosures regarding the significant
terms
of this agreement including minimum royalty payments and the
remaining life of the underlying patents.

Note 3 - Financial Statement Details - Page F-15

Inventories - Page F-17

2. We see that inventory reserves approximate 77% of inventory
cost
and that those reserves significantly increased on both an actual
and
percentage basis in 2004.  MD&A should include disclosure about
why
such a significant portion of inventory cost is reserved and your
plans for disposition of the impaired inventory.  For example,
were
any of written-off inventory items subsequently sold?  If so, were
they sold at prices above their new cost basis?  What was the
impact
of any such sales upon gross profit margins?  Please revise future
filings to address our concerns.

Note 4 - Business Combinations - Page F-18

3. We note that a significant portion of your acquisition price
related to the SynX and Epoch acquisitions was allocated to
goodwill.
In a supplemental response and in future filings provide a
description of the factors that contributed to a purchase price
that
resulted in recognition of such a significant goodwill asset.
Additionally please tell us how you determined to allocate the
excess
purchase price between goodwill, intangible assets and property,
plant and equipment.  Specifically discuss the reasons for not
allocating more of the excess purchase price to intangible assets
such as customer relationships, contracts, licenses, technology,
etc.
For reference see EITF 02-17 and Appendix A of SFAS 141.

4. In a supplemental response and in future filings please
disclose
the following:

* The types of technology you purchased from Epoch, including the
method and principal valuation assumptions.
* A condensed balance sheet that discloses the specific types of
assets and liabilities that you acquired / assumed.

      Refer to the disclosure requirements of paragraphs 51 and 52
of
SFAS 141.

SynX Pharma Inc. - Page F-18

5. We see that you have recorded a $3.8 million in-process
research
and development charge, noting that you concluded these projects
had
not reached technological feasibility and had no alternative
future
use.  In a supplemental response and in future filings please
expand
your footnote and MD&A to disclose more details regarding the
acquired IPR&D amounts, including:

* Specific nature and fair value of each significant in-process
research and development project acquired,
* Completeness, complexity and uniqueness of the project(s) at the
acquisition date,
* Nature, timing and estimated costs of the efforts necessary to
complete the project(s) as well as the expected sources of funding
therefore and anticipated completion dates,
* Risks and uncertainties associated with completing development
on
schedule and consequences if it is not completed timely and
* Significant appraisal assumptions, such as -
o period in which material net cash inflows from significant
projects
are expected to commence; and
o material anticipated changes from historical pricing, margins
and
expense levels.
In filings subsequent to the acquisition of IPR&D an update of the
status of the IPR&D projects should be provided along with details
of
any significant changes in assumptions made at the time of
acquisition and how this impacts the expected return on
investment.

Epoch Biosciences, Inc. - Page F-19

6. We see that on December 16, 2004 you acquired all the
outstanding
common stock of Epoch Biosciences, Inc. for 13.4 million shares of
your common stock.  Please supplementally demonstrate why you are
the
acquiring entity under paragraph 17 of SFAS 141.  We may have
further
comments after reviewing your response.

Note 11- Collaborative Alliances - Page F-29

Princeton BioMeditech Corporation - Page F-29

7. Please revise future filings to describe the significant terms
of
your agreement with PBM, including any minimum purchase
provisions,
license agreements, or commitments to provide additional funding.
Also disclose any payments you made during the year under this
agreement.

* * * * * * * *

      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.

	We urge all persons who are responsible for the accuracy and
adequacy of the disclosure in the filings reviewed by the staff to
be
certain that they have provided all information investors require.
Since the company and its management are in possession of all
facts
relating to a company`s disclosure, they are responsible for the
accuracy and adequacy of the disclosures they have made.

	In connection with responding to our comments, please
provide,
in writing, a statement from the company acknowledging that

* The company is responsible for the adequacy and accuracy of the
disclosure in the filings;
* Staff comments or changes to disclosure in response to staff
comments in the filings reviewed by the staff do not foreclose the
Commission from taking any action with respect to the filing; and
* The company may not assert staff comments as a defense in any
proceeding initiated by the Commission or any person under the
federal securities laws of the United States.
      In addition, please be advised that the Division of
Enforcement
has access to all information you provide to the staff of the
Division of Corporation Finance in our review of your filing or in
response to our comments on your filing.

	You may contact Eric Atallah, Staff Accountant at (202) 824-
5266
or me at (202) 942-1812 regarding comments on the financial
statements and related matters.  In this regard, do not hesitate
to
contact Angela Crane, Branch Chief, at (202) 942-1931.

      								  Sincerely,

								  Jay Webb
								  Reviewing Accountant

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Mr. Robert Saltmarsh
Nanogen, Inc.
May 2, 2005
Page 4

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