---

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UNITED STATES
SECURITIES AND EXCHANGE COMMISSIONWASHINGTON, D.C. 20549

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FORM 10-Q

|/x/ | QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|--- | ---------------------------------------------------------------------------------------

For the quarterly period ended September 30, 2001

OR

|/ / | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|--- | ----------------------------------------------------------------------------------------

For the transition period from  to

Commission File Number 000-23541

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NANOGEN, INC.(Exact name of Registrant as specified in its charter)

Delaware

33-0489621(State or other jurisdiction of
incorporation or organization)

(I.R.S. Employer
Identification No.)10398 Pacific Center Court,
San Diego, CA

92121(Address of principal executive offices)

(Zip code)


(858) 410-4600(Registrant's telephone number, including area code)

---

Indicate
by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the
preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.

YES /x/  NO / /

As of November 12, 2001, 21,563,444 shares of the Registrant's Common Stock were outstanding.

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NANOGEN, INC.  FORM 10-Q  INDEX

|              |  |                                                                                                       |  | Page
|------------- |  | ----------------------------------------------------------------------------------------------------- |  | ----
|PART I.       |  | FINANCIAL INFORMATION                                                                                 |  |     
|Item 1.       |  | Financial Statements:                                                                                 |  |     
|              |  | Consolidated Balance Sheets at September 30, 2001 and December 31, 2000                               |  | 3   
|              |  | Consolidated Statements of Operations for the Three and Nine Months ended September 30, 2001 and 2000 |  | 4   
|              |  | Consolidated Statements of Cash Flows for the Nine Months ended September 30, 2001 and 2000           |  | 5   
|              |  | Notes to Consolidated Financial Statements                                                            |  | 6   
|Item 2.       |  | Management's Discussion and Analysis of Financial Condition and Results of Operations                 |  | 10  
|Item 3.       |  | Quantitative and Qualitative Disclosures About Market Risk                                            |  | 24  
|PART II:      |  | OTHER INFORMATION                                                                                     |  |     
|Item 1.       |  | Legal Proceedings                                                                                     |  | 25  
|Item 6.       |  | Exhibits and Reports on Form 8-K                                                                      |  | 25  
|SIGNATURES    |  | 26                                                                                                   
|EXHIBIT INDEX |  | 27                                                                                                   

2

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PART I. FINANCIAL INFORMATION

Item 1. Financial Statements

NANOGEN, INC.

CONSOLIDATED BALANCE SHEETS

(in thousands, except share data)

|                                                |                                                                                                                                                                                | September 30,
2001 |        | December 31,
2000 |  
|----------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------ | ------ | ----------------- | -
|
|ASSETS                                          |                                                                                                                                                                                |                    |        |                   |  
|Current assets:                                 |                                                                                                                                                                                |                    |        |                   |  
|                                                | Cash and cash equivalents                                                                                                                                                      |                    | $      | 14,249            |  
|                                                | Short-term investments                                                                                                                                                         |                    |        | 60,816            |  
|                                                | Accounts receivable                                                                                                                                                            |                    |        | 3,581             |  
|                                                | Inventory                                                                                                                                                                      |                    |        | 4,212             |  
|                                                | Other current assets                                                                                                                                                           |                    |        | 2,534             |  
|                                                |                                                                                                                                                                                |                    |        |                   |  
|Total current assets                            |                                                                                                                                                                                |                    | 85,392 |                   |  
|Property and equipment, net                     |                                                                                                                                                                                |                    | 5,556  |                   |  
|Acquired technology rights, net                 |                                                                                                                                                                                |                    | 4,339  |                   |  
|Other assets                                    |                                                                                                                                                                                |                    | 1,286  |                   |  
|Restricted cash                                 |                                                                                                                                                                                |                    | 114    |                   |  
|                                                |                                                                                                                                                                                |                    |        |                   |  
|                                                |                                                                                                                                                                                | $                  | 96,687 |                   | $
|                                                |                                                                                                                                                                                |                    |        |                   |  
|LIABILITIES AND STOCKHOLDERS' EQUITY            |                                                                                                                                                                                |                    |        |                   |  
|Current liabilities:                            |                                                                                                                                                                                |                    |        |                   |  
|                                                | Accounts payable                                                                                                                                                               |                    | $      | 943               |  
|                                                | Accrued liabilities                                                                                                                                                            |                    |        | 3,730             |  
|                                                | Deferred revenue                                                                                                                                                               |                    |        | 681               |  
|                                                | Current portion of capital lease obligations                                                                                                                                   |                    |        | 1,191             |  
|                                                |                                                                                                                                                                                |                    |        |                   |  
|Total current liabilities                       |                                                                                                                                                                                |                    | 6,545  |                   |  
|Capital lease obligations, less current portion |                                                                                                                                                                                |                    | 1,720  |                   |  
|Other long-term liabilities                     |                                                                                                                                                                                |                    | 1,669  |                   |  
|                                                |                                                                                                                                                                                |                    |        |                   |  
|Total long-term liabilities                     |                                                                                                                                                                                |                    | 3,389  |                   |  
|Minority interest in consolidated subsidiary    |                                                                                                                                                                                |                    | 4,800  |                   |  
|Stockholders' equity:                           |                                                                                                                                                                                |                    |        |                   |  
|                                                | Convertible preferred stock, $.001 par value, 5,000,000 shares authorized; no shares issued and outstanding at September 30, 2001 and December 31, 2000                        |                    |        |                  |  
|                                                | Common stock, $.001 par value, 50,000,000 shares authorized; 21,435,211 and 20,913,151 shares issued and outstanding at September 30, 2001 and December 31, 2000, respectively |                    |        | 21                |  
|                                                | Additional paid-in capital                                                                                                                                                     |                    |        | 197,630           |  
|                                                | Accumulated other comprehensive income                                                                                                                                         |                    |        | 1,432             |  
|                                                | Deferred compensation                                                                                                                                                          |                    |        | (199              | )
|                                                | Notes receivable from officers                                                                                                                                                 |                    |        | (970              | )
|                                                | Accumulated deficit                                                                                                                                                            |                    |        | (115,961          | )
|                                                |                                                                                                                                                                                |                    |        |                   |  
|Total stockholders' equity                      |                                                                                                                                                                                |                    | 81,953 |                   |  
|                                                |                                                                                                                                                                                |                    |        |                   |  
|                                                |                                                                                                                                                                                | $                  | 96,687 |                   | $
|                                                |                                                                                                                                                                                |                    |        |                   |  

See
accompanying notes.

3

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NANOGEN, INC.

CONSOLIDATED STATEMENTS OF OPERATIONS

(unaudited)

(in thousands, except per share data)

|                                                                        |                                            | Three months ended September 30, |        | Nine months ended September 30, |  
|----------------------------------------------------------------------- | ------------------------------------------ | -------------------------------- | ------ | ------------------------------- | -
|
|Revenues:                                                               |                                            |                                  |        |                                 |  
|                                                                        | Sales                                      |                                  | $      | 1,023                           |  
|                                                                        | Sponsored research                         |                                  |        | 1,828                           |  
|                                                                        | Contract and grant revenue                 |                                  |        | 368                             |  
|                                                                        |                                            |                                  |        |                                 |  
|Total revenues                                                          |                                            |                                  | 3,219  |                                 |  
|Operating expenses:                                                     |                                            |                                  |        |                                 |  
|                                                                        | Cost of sales                              |                                  |        | 727                             |  
|                                                                        | Research and development                   |                                  |        | 4,824                           |  
|                                                                        | Selling, general and administrative        |                                  |        | 6,194                           |  
|                                                                        | Litigation and settlement of patent matter |                                  |        | 123                             |  
|                                                                        |                                            |                                  |        |                                 |  
|Total operating expenses                                                |                                            |                                  | 11,868 |                                 |  
|                                                                        |                                            |                                  |        |                                 |  
|Loss from operations                                                    |                                            |                                  | (8,649 | )                               |  
|Interest income, net                                                    |                                            |                                  | 1,019  |                                 |  
|Minority interest in loss of consolidated subsidiary                    |                                            |                                  | 485    |                                 |  
|Other income                                                            |                                            |                                  | 125    |                                 |  
|                                                                        |                                            |                                  |        |                                 |  
|Net loss                                                                |                                            | $                                | (7,020 | )                               | $
|                                                                        |                                            |                                  |        |                                 |  
|Net loss per sharebasic and diluted                                    |                                            | $                                | (0.33  | )                               | $
|                                                                        |                                            |                                  |        |                                 |  
|Number of shares used in computing net loss per sharebasic and diluted |                                            |                                  | 21,206 |                                 |  
|                                                                        |                                            |                                  |        |                                 |  

See
accompanying notes.

4

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NANOGEN, INC.

CONSOLIDATED STATEMENTS OF CASH FLOWS

(unaudited)

(in thousands)

|                                                                     |                                                                                  | Nine months ended September 30,                                  |                    
|-------------------------------------------------------------------- | -------------------------------------------------------------------------------- | ---------------------------------------------------------------- | -------------------
|
|Operating activities:                                                |                                                                                  |                                                                  |                    
|                                                                     | Net loss                                                                         |                                                                  | $                  
|                                                                     | Adjustments to reconcile net loss to net cash used in operating activities:      |                                                                  |                    
|                                                                     |                                                                                  | Issuance of common stock pursuant to settlement of patent matter |                    
|                                                                     |                                                                                  | Depreciation and amortization                                    |                    
|                                                                     |                                                                                  | Amortization related to short-term investments                   |                    
|                                                                     |                                                                                  | Stock based compensation expense                                 |                    
|                                                                     |                                                                                  | Interest capitalized on notes receivables from officers          |                    
|                                                                     |                                                                                  | Cumulative foreign currency translation gain                     |                    
|                                                                     |                                                                                  | Minority interest in loss of consolidated subsidiary             |                    
|                                                                     |                                                                                  | Gain on sale of short-term investments                           |                    
|                                                                     |                                                                                  | Changes in operating assets and liabilities:                     |                    
|                                                                     |                                                                                  |                                                                  | Accounts receivable
|                                                                     |                                                                                  |                                                                  | Inventory          
|                                                                     |                                                                                  |                                                                  | Other assets       
|                                                                     |                                                                                  |                                                                  | Accounts payable   
|                                                                     |                                                                                  |                                                                  | Accrued liabilities
|                                                                     |                                                                                  |                                                                  | Deferred revenue   
|                                                                     |                                                                                  |                                                                  |                    
|Net cash used in operating activities                                |                                                                                  |                                                                  | (25,903            
|Investing activities:                                                |                                                                                  |                                                                  |                    
|                                                                     | Purchase of short-term investments                                               |                                                                  |                    
|                                                                     | Proceeds from sale of short-term investments                                     |                                                                  |                    
|                                                                     | Purchase of equipment                                                            |                                                                  |                    
|                                                                     | Purchase of technology rights                                                    |                                                                  |                    
|                                                                     |                                                                                  |                                                                  |                    
|Net cash used in investing activities                                |                                                                                  |                                                                  | (19,804            
|Financing activities:                                                |                                                                                  |                                                                  |                    
|                                                                     | Principal payments on capital lease obligations                                  |                                                                  |                    
|                                                                     | Proceeds from development partner                                                |                                                                  |                    
|                                                                     | Proceeds from minority interest shareholder in joint venture                     |                                                                  |                    
|                                                                     | Issuance of common stock, net of repurchases                                     |                                                                  |                    
|                                                                     | Note receivable payments from officers                                           |                                                                  |                    
|                                                                     | Reduction of restricted cash balance                                             |                                                                  |                    
|                                                                     |                                                                                  |                                                                  |                    
|Net cash provided by financing activities                            |                                                                                  |                                                                  | 4,443              
|                                                                     |                                                                                  |                                                                  |                    
|Effect of exchange rate changes                                      |                                                                                  |                                                                  | 183                
|                                                                     |                                                                                  |                                                                  |                    
|Net (decrease) increase in cash and cash equivalents                 |                                                                                  |                                                                  | (41,081            
|Cash and cash equivalents at beginning of period                     |                                                                                  |                                                                  | 55,330             
|                                                                     |                                                                                  |                                                                  |                    
|Cash and cash equivalents at end of period                           |                                                                                  | $                                                                | 14,249             
|                                                                     |                                                                                  |                                                                  |                    
|Supplemental disclosure of cash flow information:                    |                                                                                  |                                                                  |                    
|                                                                     | Interest paid                                                                    |                                                                  | $                  
|                                                                     |                                                                                  |                                                                  |                    
|Supplemental schedule of noncash investing and financing activities: |                                                                                  |                                                                  |                    
|                                                                     | Equipment acquired under capital leases                                          |                                                                  | $                  
|                                                                     |                                                                                  |                                                                  |                    
|                                                                     | Unrealized gain on short-term investments                                        |                                                                  | $                  
|                                                                     |                                                                                  |                                                                  |                    
|                                                                     | Warrant issued for research & development collaboration, net of assets received  |                                                                  | $                  
|                                                                     |                                                                                  |                                                                  |                    
|                                                                     | Payment and cancellation of notes receivable                                     |                                                                  | $                  
|                                                                     |                                                                                  |                                                                  |                    
|                                                                     | Payment for services and cancellation of restricted stock                        |                                                                  | $                  
|                                                                     |                                                                                  |                                                                  |                    
|                                                                     | Common stock issued in connection with employee benefit plan, net of forfeitures |                                                                  | $                  
|                                                                     |                                                                                  |                                                                  |                    

See accompanying notes.

5

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NANOGEN, INC.

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

(unaudited)

September 30, 2001

1. Basis of Presentation

The accompanying unaudited consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United
States of America for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not
include all of the information and footnotes required by accounting principles generally accepted in the United States of America for complete financial statements. The consolidated balance sheet as
of September 30, 2001, consolidated statements of operations for the three and nine months ended September 30, 2001 and 2000, and the consolidated statements of cash flows for the nine
months ended September 30, 2001 and 2000 are unaudited, but include all adjustments (consisting of normal recurring adjustments) which the Company considers necessary for a fair presentation of
the financial position, results of operations and cash flows for the periods presented. The results of operations for the three and nine months ended September 30, 2001 shown herein are not
necessarily indicative of the results that may be expected for the year ending December 31, 2001.

Certain
prior year amounts have been reclassified to conform to the current year presentation.

For
more complete financial information, these financial statements, and notes thereto, should be read in conjunction with the audited consolidated financial statements for the year
ended December 31, 2000 included in the Nanogen, Inc. Form 10-K, filed with the Securities and Exchange Commission.



The Company computes net income per share in accordance with SFAS No. 128, "Earnings per Share." Under the provisions of SFAS No. 128, basic net
income (loss) per share is computed by dividing the net income (loss) available to common stockholders for the period by the weighted average number of common shares outstanding during the period.
Diluted net income (loss) per share is computed by dividing the net income (loss) for the period by the weighted average number of common shares outstanding during the period and dilutive common
shares outstanding computed using the treasury stock method. Weighted average common shares outstanding during the period does not include shares issued pursuant to the exercise of stock options prior
to vesting and shares issued under the Company's 401K benefit plan prior to vesting. Due to the losses incurred by the Company during the three and nine months ended September 30, 2001 and
2000, common stock equivalents resulting from the assumed exercise of outstanding stock options and warrants have been excluded from the computation of diluted net loss per share as their effect would
be anti-dilutive.



In July 2001, the Financial Accounting Standards Board ("FASB") issued FASB Statements Nos. 141 and 142 (FAS 141 and FAS 142), "Business
Combinations" and "Goodwill and Other Intangible Assets." FAS 141 replaces APB 16 and eliminates pooling-of-interests accounting prospectively. It also provides guidance
on purchase accounting related to the recognition of intangible assets and accounting for negative goodwill. FAS 142 changes the accounting for goodwill from an amortization method to an
impairment-only approach. Under FAS 142, goodwill will be tested annually and whenever events or circumstances occur indicating that goodwill might be impaired. FAS 141 and
FAS 142 are effective for all business combinations completed after June 30, 2001. Upon adoption of FAS 142, amortization of goodwill recorded for business combinations
consummated prior to July 1, 2001 will cease, and intangible assets acquired prior to July 1, 2001 that do not meet the criteria for recognition under FAS 141 will be reclassified
to goodwill. Companies are required to adopt FAS 142 for fiscal years beginning after December 15, 2001. The adoption of these standards is not expected to have a material impact on the
Company's results of operations and financial position.

6

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2. Inventory

Inventory consists of the following (in thousands):

September 30,
2001

December 31,
2000Raw materials

$
554

$
288Work in process


1,404


491Finished goods


2,254


1,510$
4,212

$
2,289


Finished
goods include NanoChip® Molecular Biology Workstations ("NanoChip® Workstations") that are installed at customer sites where title has not transferred
to the customer.

The
Company's manufacturing agreement with Hitachi, Ltd. ("Hitachi") requires that the Company provide annual purchase commitments to Hitachi for NanoChip®
Workstations. As of September 30, 2001, the Company has commitments to purchase approximately $4.0 million in NanoChip® Workstations through March 31, 2002.

3. Comprehensive Loss

SFAS No. 130, Reporting Comprehensive Income, requires the Company to report, in addition to net income, comprehensive income (loss) and its components.
A summary is as follows:

Consolidated Statements of Comprehensive Loss
(unaudited)

Three months ended September 30,

Nine months ended September 30,2001

2000

2001

2000Comprehensive loss:Net unrealized gain on sale of investments

$
549

$
8

$
1,141

$
8Foreign currency translation gain


21





21


Net loss


(7,020
)

(4,579
)

(25,049
)

(12,370
)Comprehensive loss

$
(6,450
)
$
(4,571
)
$
(23,887
)
$
(12,362
)


4. Collaborative Alliances



In September 1999, the Company entered into two technology development programs with Aventis Research and Technologies, an affiliate of Hoechst AG
("Aventis"), which focus on the development of gene expression tools utilizing electronic bioarrays and the development of high throughput screening tools for protein kinase analyses. In total, these
two programs may provide a maximum of $12.0 million in funding to the Company through December 31, 2001. As of September 30, 2001, the Company had received an aggregate of
$9.2 million in funding for these programs, including an up-front initiation fee of $2.0 million that was received in the fourth quarter of 1999.

Revenue
is primarily recognized under these agreements as expenses are incurred, and totaled $1.5 million and $5.4 million for the three and nine months ended
September 30, 2001, respectively, and $2.1 million and $5.7 million for the three and nine months ended September 30, 2000, respectively. Funding received in advance of
incurred expenses is recorded as deferred revenue until the expenses are incurred. Deferred revenues were $123,000 at December 31, 2000. There were no deferred revenues at September 30,
2001.

7

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In June 2001, the Company entered into agreements with Aventis to create a new company, Nanogen Recognomics GmbH ("Nanogen Recognomics"). The joint venture was established to
develop new products and applications for the NanoChip® System. Nanogen Recognomics is sixty percent owned by the Company and forty percent owned by Aventis and is based in Frankfurt,
Germany. Aventis will provide the first $5 million of funding for the operations of the new company and also contributed intellectual property in the form of eighteen patents. The Company is
required to spend an aggregate of $5.5 million, at the rate of $1.1 million per year beginning April 1, 2001, for its own general technology development which benefits the
commercialization and development of potential joint venture products. In addition, Nanogen Recognomics will own several patent applications filed jointly by the Company and Aventis. The Company has
licensed certain aspects of its NanoChip® technology to the new company and will seek to commercialize new products and applications developed by the joint venture. Aventis retains the
right to utilize the former Aventis patent portfolio in fields outside of the joint venture. In conjunction with the agreement to form Nanogen Recognomics, the Company issued a warrant to Aventis to
purchase 315,863 shares of common stock exercisable through July 17, 2006 at an agreed upon price of $9.828. The value of this warrant, as determined by the Black-Scholes valuation model, equal
to $1.2 million, is included in other assets in the accompanying consolidated financial statements and will be amortized over a two and a half year period.

The
results of operations for Recognomics are fully consolidated in the financial statements included herein. Total operating costs of Recognomics are reflected in research and
development expenses and totaled $547,000 for the three and nine months ended September 30, 2001.

Hitachi, Ltd.

In July 2000, the Company executed a ten-year agreement with Hitachi, Ltd., Nissei Sangyo Co. Ltd. and Hitachi Instruments
Service Co. Ltd. of Japan (collectively, "Hitachi") to develop, manufacture and distribute additional potential products based on the parties' proprietary technologies, potentially including,
among other things, reduced-size instruments for genetic testing, integrated amplification and point-of-care detection. The agreement provides that the parties will
jointly determine which projects to prioritize over the term of the agreement. The agreement may be terminated before its expiration by either party, subject to various restrictions. Pursuant to the
terms of the agreement, Hitachi and the Company each may contribute up to $28.5 million in cash over the ten-year period. The agreement requires that 50% of the total contributions
made by Hitachi be repaid by applying a percentage to the Company's gross NanoChip® Cartridge sales until the liability is paid in full. This obligation is
non-interest bearing and is not collateralized by any assets held by the Company. The total amount due to Hitachi at September 30, 2001 was $1.6 million. In addition, Hitachi
made an equity investment in the Company by purchasing 74,590 shares of the Company's common stock worth approximately $2.0 million pursuant to a private sale by the Company based at a per
share price of $26.813 (the fair market value as of the signing date of the Hitachi agreement). The agreement expands on the agreement executed by the Company and Hitachi in January 2000.
Hitachi has the right to be the exclusive distributor of collaboration products in Japan and, based upon the attainment of minimum sales targets to be mutually agreed upon, in other Asian countries.
The Company retains the exclusive right to distribute collaboration products outside of these countries. The agreement is non-exclusive and excludes some clinical markets.

5. Litigation

In July 2001, the Company entered into a settlement agreement with Motorola, Genometrix, and MIT concluding the declaratory judgment action by the
Company against Motorola, Genometrix and MIT and Motorola's counterclaim against the Company. In connection with the settlement, the Company has secured a license from Motorola to certain claims of
the '939 Patent. In exchange, the Company made a one-time payment of $2.5 million in cash and issued 416,666 shares of the Company's

8

---

common stock (valued at approximately $2.5 million based upon a per share price of $6.00, the fair market value on the date of settlement) to the parties involved. The settlement does not
include any cross-licensing provisions of the Company's technology to Motorola, Genometrix or MIT. The lawsuit and the counterclaim have now been dismissed.

In
November 2000, the Company filed a complaint against CombiMatrix Corp. ("CombiMatrix") and Dr. Donald Montgomery in the United States District Court for the Southern
District of California. Dr. Montgomery is a former company employee now affiliated with CombiMatrix. The Company's complaint alleges that the naming of Dr. Montgomery as the sole
inventor on U.S. Patent No. 6,093,302, entitled "Electrochemical Solid Phase Synthesis" (the "'302 patent"), and assignment of the '302 patent to CombiMatrix were incorrect and that the
invention was made by company employees. The complaint also alleges that inventions disclosed in the patent were the Company's trade secrets and that CombiMatrix and Dr. Montgomery
misappropriated these trade secrets by their actions, including publishing those trade secrets in patent applications. The Company's complaint seeks correction of inventorship, assignment of rights in
the patent to the Company, an injunction preventing disclosure of trade secrets and damages for trade secret misappropriation.

In
December 2000, CombiMatrix and Dr. Montgomery filed a motion to dismiss the Company's complaint. In January 2001, the motion was denied as to all claims except
a claim for conversion, as to which the motion was granted without prejudice. The Company elected not to amend its complaint as to the conversion claim. On March 9, 2001, CombiMatrix and
Dr. Montgomery answered the Company's complaint, asserted various affirmative defenses and filed a counterclaim for breach of contract against
the Company for unspecified damages allegedly arising from the filing of the complaint at a time when CombiMatrix had announced its intent to make an initial public offering of its shares. The
counterclaim asserts that the Company, by filing its complaint, breached a settlement agreement entered into between the Company and Dr. Montgomery in 1995. On May 14, 2001, the Company
filed a motion to dismiss CombiMatrix's counterclaim, which was denied on July 27, 2001. Discovery is currently ongoing.

No
assurances can be given that the Company will prevail in the lawsuit or that it can successfully defend itself against the counterclaim. The Company is expending considerable
financial resources and managerial efforts prosecuting the lawsuit and defending against Dr. Montgomery's and CombiMatrix's counterclaim. The Company may not prevail in the action, which could
have a material adverse effect on the Company.

9

---



Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations

This report includes forward-looking statements about our business and results of operations that are subject to risks and uncertainties that could cause our
actual results to vary materially from those reflected in the forward-looking statements. Words such as "believes," "anticipates," "plans," "estimates," "future," "could," "may," "should," "expect,"
"envision," "potentially," variations of such words and similar expressions are intended to identify such forward-looking statements. Factors that could cause or contribute to these differences
include those discussed below under the caption "Factors that May Affect Results" and elsewhere in this Form 10-Q. Readers are cautioned not to place undue reliance on these
forward-looking statements, which speak only as of the date hereof. We disclaim any intent or obligation to update these forward-looking statements.

Overview

We integrate advanced microelectronics and molecular biology into a core technology platform with potentially broad and diverse commercial applications in the
fields of genomics, biomedical research, medical diagnostics, drug discovery, forensics, agriculture, environmental testing, biowarfare, human identification and potentially the electronics and
telecommunications industries. The first application we have developed, the NanoChip® System, is an integrated bioassay system consisting of the NanoChip® Molecular Biology
Workstation and the NanoChip® Cartridge. The NanoChip® Workstation is comprised of two automated instruments and the NanoChip® Cartridge, a consumable cartridge,
which incorporates a proprietary microchip. The NanoChip® System provides a flexible tool for the rapid identification and precision analysis of biological test samples containing charged
molecules.

Since
commencing operations in 1993, we have applied substantially all of our resources to our research and development programs, and, since early 2000, to our commercial launch of
the NanoChip® System. We have incurred losses since inception and, as of September 30, 2001, had an accumulated deficit of $116.0 million. We expect to incur significant
losses over at least the next several years as we continue our research and product development efforts and attempt to further commercialize our products.

We
believe our future operating results may be subject to quarterly fluctuations due to a variety of factors, including, but not limited to, the achievement of milestones under our
collaborative agreements, whether and when new products are successfully developed and introduced by us or our competitors, market acceptance of the NanoChip® System and potential products
under development, and the type of acquisition program our potential customers choose. Payments under contracts, grants and sponsored research agreements will be subject to significant fluctuations in
both timing and amount
and therefore our results of operations for any period may not be comparable to the results of operations for any other period.

Results of Operations

Revenues.For the three and nine months ended September 30, 2001 sales totaled $1.0 million and
$1.6 million, respectively, compared to $545,000 and $709,000 for the three and nine months ended September 30, 2000, respectively. Sales revenue during the three and nine months ended
September 30, 2001 includes the sale of seven and ten NanoChip® Molecular Biology Workstations, respectively, through outright sales transactions where the title of the instrument
passed to the customer as well as sales of NanoChip® Cartridges. Sales revenue for the three and nine months ended September 30, 2000 was comprised of the sale of five and six
NanoChip® Molecular Biology Workstations, respectively, as well as sales of NanoChip® Cartridges. We offer our products to customers under several different types of
acquisition programs, some of which do not pass title to the customer, and for which no revenue is recorded at the time of delivery. In these cases, revenue, if any, will be recorded

10

---

ratably over the rental period. Our sales revenue may vary from quarter to quarter due to, among other things, the types of acquisition programs our potential customers may choose.

For
the three and nine months ended September 30, 2001 revenues from sponsored research totaled $1.8 million and $6.2 million, respectively, compared to
$2.6 million and $6.1 million for the three and nine months ended September 30, 2000, respectively. Revenues are primarily recorded under these arrangements as expenses are
incurred. Payments received in advance under these arrangements are recorded as deferred revenue until the expenses are incurred. Sponsored research revenue recognized during the three and nine months
ended September 30, 2001, was primarily earned in connection with our technology development programs under our research and development agreement entered into in September 1999 with
Aventis and our development program entered into in July 2000 with Hitachi. Additionally, sponsored research revenue recognized during the nine months ended September 30, 2001 includes
the sale of two NanoChip® Workstations funded under one of the Aventis research programs. Sponsored research revenue recognized during the three and nine months ended September 30,
2000, was earned in connection with the research and development agreements entered into in December 1998 and September 1999 with Aventis and includes the sale of one
NanoChip® Workstations funded under one of the Aventis research programs.

We
fund some of our research and development efforts through contracts and grants awarded by various federal and state agencies. Revenues are recognized under these contracts and
grants as expenses are incurred.

Continuation
of sponsored research agreements, contracts and grants is dependent upon us achieving specific contractual milestones. Our current technology programs under our research
and development agreement with Aventis are anticipated to conclude prior to December 31, 2001. The recognition of revenue under sponsored research agreements, contracts and grants may vary from
quarter to quarter and may result in significant fluctuations in operating results from year to year.

Gross Margins.Gross margins for the three and nine months ended September 30, 2001 were 28.9% and 27.5%,
respectively, and were impacted by the sale of NanoChip® Workstations to distributors at a discount from list price. In addition, gross margins during these periods in 2001 were impacted
by underabsorbed overhead costs due to underutilized capacity. As we are still in the early stages of our first product launch, we expect to continue to incur significant costs associated with excess
production capacity during 2001. For the three months ended September 30, 2000, gross margin was 19.8% and was unfavorably impacted by sales to certain customers under various discount
programs. During the nine months ended September 30, 2000 our gross margin was 36.5% and was favorably impacted by the sale of one NanoChip® Workstation for which the cost had been
recognized as research and development expense in a prior period as the Workstation was a prototype unit.

Research and Development Expenses.For the three and nine months ended September 30, 2001, research and
development expenses totaled $4.8 million and $14.0 million, respectively, compared to $5.4 million and $14.2 million for the three and nine months ended
September 30, 2000, respectively. During these periods, research and development expenses included salaries for scientific, engineering and operations personnel, costs associated with improving
and refining our current products as well as development of potential new products, protocols, lab supplies, consulting, travel, facilities, and other expenditures associated with our research and
product development activities. We anticipate that we will continue to invest in research and product development at approximately this same level for the foreseeable future.

Selling, General and Administrative Expenses.For the three and nine months ended September 30, 2001, selling,
general and administrative expenses totaled $6.2 million and $16.4 million, respectively, compared to $4.0 million and $9.7 million for the three and nine months ended
September 30, 2000, respectively. The increase is primarily due to costs associated with the expansion,

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development and support of our sales and marketing organization. In addition, during the three months ended September 30, 2001, we recorded a provision of $918,000 for inventory used in sales
and marketing activities. With the exception of the expense related to this provision, selling, general and administrative expenses are expected to continue at the current level for the foreseeable
future as we continue to market and sell our current products.

Litigation and Settlement of Patent Matter.For the three and nine months ended September 30, 2001, litigation
and settlement of a patent matter totaled $123,000 and $6.4 million, respectively. For the three and nine months ended September 30, 2000, we did not incur significant costs related to
the settlement of this patent matter. Costs incurred during the three and nine month period ended September 30, 2001 primarily consist of the settlement fee of $5.0 million in addition
to legal fees incurred related to the litigation process. In July 2001, a settlement agreement was reached with Motorola, Inc., Genometrix, Inc. and the Massachusetts Institute of
Technology concluding the declaratory judgment action by us against Motorola, Genometrix and MIT as well as Motorola's counterclaim against us. In connection with the settlement, we paid a total of
$5.0 million to the parties in the form of $2.5 million in cash and 416,666 shares of our common stock (valued at approximately $2.5 million based upon a per share price of $6.00,
the fair market value on the date of settlement).

Interest Income, Net.For the three and nine months ended September 30, 2001, net interest income totaled
$1.0 million and $3.4 million, respectively, compared to $1.8 million and $3.7 million for the three and nine months ended September 30, 2000, respectively. The
decrease in net interest income is a result of lower average cash balances as well as lower yields on outstanding cash balances during the three months ended September 30, 2001 compared to the
same period in 2000.

Minority Interest in Loss of Consolidated Subsidiary.For the three and nine months ended September 30, 2001
minority interest in consolidated subsidiary totaled $485,000. The net loss primarily consists of salaries for scientific and engineering personnel and other costs associated with the development of
new products and applications for the NanoChip® System incurred by Nanogen Recognomics, our joint venture with Aventis. Operating costs incurred by Nanogen Recognomics are funded by
Aventis and are reflected in research and development expenses in the consolidated financial statements included herein.

Liquidity and Capital Resources

At September 30, 2001, we had $75.1 million in cash, cash equivalents and short-term investments, compared to $95.1 million at
December 31, 2000. The decrease is primarily due to cash used in operations during the nine months ended September 30, 2001.

Net
cash used in operating activities was $25.9 million and $15.6 million for the nine months ended September 30, 2001 and 2000, respectively. Cash used for
operations during the nine months ended September 30, 2001 was primarily related to costs associated with our expanded sales and marketing organization as the launch of our initial products
progresses, $1.4 million in patent litigation fees, legal fees related to establishing, maintaining and defending our intellectual property portfolio, and supporting our continued research and
development efforts. In addition, our accounts receivable balance increased by $2.3 million primarily as a result of product and sponsored research revenue recorded during the three months
ended September 30, 2001. During the nine months ended September 30, 2001, our inventory balance increased by $1.9 million primarily due to scheduled purchases of
NanoChip® Molecular Biology Workstations under our manufacturing arrangement with Hitachi, Ltd. ("Hitachi").

Net
cash provided by financing activities was $4.4 million and $78.2 million for the nine months ended September 30, 2001 and 2000, respectively. Cash provided by
financing activities during the nine months ended September 30, 2001 was primarily related to proceeds received from Aventis for the

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operations of our newly formed joint venture, Nanogen Recognomics, totaling $4.8 million. In addition, $1.1 million in proceeds were received in connection with our development program
entered into in July 2000 with Hitachi offset by cash used for payments on our capital leases. Cash provided by financing activities during the nine months ended September 30, 2000 was
primarily due to our follow-on public offering of common stock in March 2000 generating net proceeds of $76.5 million.

We
fund most of our equipment acquisitions and leasehold improvements through capital leasing facilities. During the first nine months of 2001, we financed approximately
$1.3 million of capital equipment, compared to approximately $622,000 during the same period in 2000. We anticipate that we will continue to use capital equipment leasing or debt facilities to
fund most of our equipment acquisitions and leasehold improvements.

Our
manufacturing agreement with Hitachi, Ltd. requires that we provide annual purchase commitments to Hitachi for NanoChip® Molecular Biology Workstations. As of
September 30, 2001, we have commitments to purchase approximately $4.0 million in NanoChip® Workstations through March 31, 2002.

We
expect that our existing capital resources, combined with anticipated revenues from potential product sales, reagent rentals, leases or other types of acquisition programs for the
NanoChip® System, sponsored research agreements and contracts and grants will be sufficient to support our planned operations through at least the next two years. This estimate of the
period for which we expect our available sources of liquidity to be sufficient to meet our capital requirements is a forward-looking statement that involves risks and uncertainties, and actual results
may differ materially. Our future liquidity and capital funding requirements will depend on numerous factors including, but not limited to, the extent to which our products are successfully developed
and gain market acceptance, the timing of regulatory actions regarding our potential products, the costs and timing of expansion of sales, marketing and manufacturing activities, prosecution and
enforcement of patents important to our business and any litigation related thereto, the results of clinical trials, competitive developments, and our ability to maintain existing collaborations and
to enter into additional collaborative arrangements. We have incurred negative cash flow from operations since inception and do not expect to generate positive cash flow to fund our operations for at
least the next two years. We may need to raise additional capital to fund our research and development programs, to scale up manufacturing activities and expand our sales and marketing efforts to
support the commercialization of our other products or applications under development. Additional capital may not be available on terms acceptable to us, or at all. If adequate funds are not
available, we may be required to curtail our operations significantly or to obtain funds through entering into collaborative agreements or other arrangements on unfavorable terms. Our failure to raise
capital on acceptable terms when needed could have a material adverse effect on our business, financial condition or results of operations.

Factors that May Affect Results

Our products may not be successfully developed or commercialized, which would harm us and force us to curtail or cease operations.

We are at an early stage of development. We currently have only two products for sale, our NanoChip® Molecular Biology Workstation and our
NanoChip® Cartridge. All of our other potential products are under development. Our NanoChip® System or our other products may not be successfully developed or commercialized
on a timely basis, or at all. If we are unable, for technological or other reasons, to complete the development, introduction or scale-up of manufacturing of our new products, or if our
products do not achieve a significant level of market acceptance, we would be forced to curtail or cease operations.

Our
success will depend upon our ability to overcome significant technological challenges and successfully introduce our products into the marketplace. A number of applications
envisioned by us

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will require significant enhancements to our basic technology platform. There can be no assurance that we can successfully develop such enhancements.

Lack of market acceptance of our technology would harm us.

We may not be able to develop commercially viable products. Even if we develop a product it may not be accepted in the marketplace. If we are unable to achieve
market acceptance, we will not be able to generate sufficient product revenue to become profitable. We may also be forced to carry greater inventories of our products for longer periods than we may
have anticipated. If we are unable to sell our inventory of our products in a timely fashion and at anticipated price levels, we may not become profitable. In addition, we may have to take accounting
charges and reduce the value of our product inventory to its net realizable value. Market acceptance will depend on many factors, including our ability to:



In
addition, our technology platform could be harmed by limited funding available for product and technology acquisitions by our customers, internal obstacles to customer approvals of
purchases of our products and market conditions in general.

Commercialization of some of our potential products depends on collaborations with others. If our collaborators are not successful or if we are unable
to find collaborators in the future, we may not be able to develop these products.

Our strategy for the research, development and commercialization of some of our products requires us to enter into contractual arrangements with corporate
collaborators, joint venture partners, licensors, licensees and others. Our success depends in part upon the performance by these collaboration partners and potential collaboration partners of their
responsibilities under these arrangements. Some collaborators may not perform their obligations as we expect or we may not derive any revenue or other benefits from these arrangements.

We
have collaborative agreements with a health care company, a pharmaceutical company and a developer and manufacturer of instrumentation products and we entered into a joint venture
with the research and development subsidiary of a pharmaceutical company. We do not know whether the collaborators will successfully develop and market any products under our respective agreements.
Moreover, some of our collaborators are also researching competing technologies targeted by our collaborative programs. We may be unsuccessful in entering into other collaborative arrangements to
develop and commercialize our products. In addition, disputes may arise over ownership rights to intellectual property, know-how or technologies developed with our collaborators.

We
currently have agreements with Aventis, Becton Dickinson and Hitachi that contemplate the commercialization of products resulting from the agreements between the parties. In
addition, we have a manufacturing and distribution agreement with Hitachi. In June 2001 we also entered into a joint venture, Nanogen Recognomics GmbH, with Aventis Research and
Technologies & Co. KG, in which we own 60% of the stock of Nanogen Recognomics and Aventis R&T owns the remaining 40%. Nanogen Recognomics seeks to combine our NanoChip® technology
and Aventis R & T's intellectual property and expertise in synthetic oligonucleotide chemistry and advanced molecular biology to develop new products and applications for the
NanoChip® System. These collaborations may not be successful.

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We have a history of net losses. We expect to continue to incur net losses and we may not achieve or maintain profitability.

We began selling our first two products in the second quarter of 2000, but we did not sell significant quantities of our first products during fiscal 2000 or
during the nine months ended September 30, 2001. From our inception to September 30, 2001, we have incurred cumulative net losses totaling approximately $116.0 million. Moreover,
our negative cash flow and losses from operations will continue to increase for the foreseeable future. We may never generate sufficient product revenue to become profitable. We also expect to have
quarter-to-quarter fluctuations in revenues, expenses and losses, some of which could be significant. The amount and timing of product revenue recognition may depend on whether
potential customers for the NanoChip® System choose to enter into title transfer or non-title transfer transactions.

To
develop and sell our products successfully, we will need to increase our spending levels in research and development, as well as in selling, marketing and administration. We will
have to incur these increased spending levels before knowing whether our products can be sold successfully.

We may need additional capital in the future. If additional capital is not available, we may have to curtail or cease operations.

We may need to raise more money to continue the research and development necessary to bring our products to market and to establish manufacturing and marketing
capabilities. We may seek additional funds through public and private stock offerings, arrangements with corporate partners, borrowings under lease lines of credit or other sources. If we cannot raise
more money we will have to reduce our capital expenditures, scale back our development of new products, reduce our workforce and license to others products or technologies that we otherwise would seek
to commercialize ourselves. The amount of money we will need will depend on many factors, including among others:





Additional
capital may not be available on terms acceptable to us, or at all. Any additional equity financing may be dilutive to stockholders, and debt financing, if available, may
include restrictive covenants.

Competing technologies may adversely affect us.

We expect to encounter intense competition from a number of companies that offer products in our targeted application areas. We anticipate that our competitors
in these areas will include:



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If
we are successful in developing products in these areas, we will face competition from established companies and numerous development-stage companies that continually enter these
markets. In many instances, our competitors have substantially greater financial, technical, research and other resources and larger, more established marketing, sales, distribution and service
organizations than us. Moreover,
these competitors may offer broader product lines and have greater name recognition than us and may offer discounts as a competitive tactic.

In
addition, several development-stage companies are currently making or developing products that compete with or will compete with our potential products. Our competitors may succeed
in developing, obtaining FDA approval or marketing technologies or products that are more effective or commercially attractive than our potential products, or that render our technologies and
potential products obsolete.

As
these companies develop their technologies, they may develop proprietary positions that may prevent us from successfully commercializing products.

Also,
we may not have the financial resources, technical expertise or marketing, distribution or support capabilities to compete successfully in the future.

The uncertainty of patent and proprietary technology protection may adversely affect us.

Our success will depend in part on obtaining and maintaining meaningful patent protection on our inventions, technologies and discoveries. Our ability to
compete effectively will depend on our ability to develop and maintain proprietary aspects of our technology, and to operate without infringing the proprietary rights of others, or to obtain rights to
third-party proprietary rights, if necessary. Our pending patent applications may not result in the issuance of patents. Our patent applications may not have priority over others' applications, and
even if issued, our patents may not offer protection against competitors with similar technologies. Any patents issued to us may be challenged, invalidated or circumvented and the rights created
thereunder may not afford us a competitive advantage.

We
also rely upon trade secrets, technical know-how and continuing inventions to develop and maintain our competitive position. Others may independently develop
substantially equivalent proprietary information and techniques or otherwise gain access to our trade secrets or disclose our technology and we may not be able to meaningfully protect our trade
secrets, or be capable of protecting our rights to our trade secrets. We seek to protect our technology and patents, in part, by confidentiality agreements with our employees and contractors. Our
employees may breach their existing Proprietary Information, Inventions, and Dispute Resolution Agreements and these agreements may not protect our intellectual property. This could have a material
adverse effect on us.

Our products could infringe on the intellectual property rights of others, which may subject us to future litigation and cause us to be unable to
license technology from third parties.

Our commercial success also depends in part on us neither infringing valid, enforceable patents or proprietary rights of third parties, nor breaching any
licenses that may relate to our technologies and products. We are aware of other third-party patents that may relate to our technology. It is possible that we may unintentionally infringe these
patents or other patents or proprietary rights of third parties. We may in the future receive notices claiming infringement from third parties as well as invitations to take licenses under third-party
patents. Any legal action against us or our collaborative partners claiming damages and seeking to enjoin commercial activities relating to our products and processes affected by third-party rights
may require us or our collaborative partners to obtain licenses in order to continue to manufacture or market the affected products and processes. In addition, these actions may subject us to
potential liability for damages. We or our collaborative partners may not prevail in an action and any license required under a patent may not be made available on commercially acceptable terms, or at
all.

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There are many U.S. and foreign patents and patent applications held by third parties in our areas of interest, and we believe that, besides our current litigation with CombiMatrix
and Dr. Montgomery described below, there may be significant other litigation in the industry regarding patent and other intellectual property rights. Additional litigation could result in
substantial costs and the diversion of management's efforts regardless of the result of the litigation. Additionally, the defense and prosecution of interference proceedings before the U.S. Patent and
Trademark Office, or USPTO, and related administrative proceedings would result in substantial expense to us and significant diversion of effort by our technical and management personnel. We may in
the future become subject to USPTO interference proceedings to determine the priority of inventions. In addition, laws of some foreign countries do not protect intellectual property to the same extent
as do laws in the U.S., which may subject us to additional difficulties in protecting our intellectual property in those countries.

We
are aware of U.S. and corresponding foreign patents and applications which are assigned to Affymax Technologies, N.V., and Affymetrix, Inc. which relate to certain devices
having 1,000 or more groups of oligonucleotides occupying a total area of less than 1 cm2, 400 different oligonucleotides per cm2 on a substrate, and for gene expression,
more than 100 different oligonucleotides at a density greater than about 60 different oligonucleotides per 1 cm2. In the event that we proceed with the development of arrays with more
than 400 groups of oligonucleotides, or for gene expression, with more than 100 different oligonucleotides, we expect to design our devices through, among other things, the selection of the physical
dimensions, methods of binding, selection of support materials and intended uses of the device to avoid infringing these patents. We may not be able to design around these patents. We are aware of
U.S. and European patents and patent applications owned by Isis Innovations Ltd. or Isis Innovations (E. M. Southern). We have opposed one allowed European patent which had broad claims to
array technology for analyzing a predetermined polynucleotide sequence. Isis Innovations' position with respect to the opposed patent is that the claims relate to what it terms the "diagnostic mode."
Those claims have now all been narrowed to the point that if the claims are accepted by the European Patent Office, they would not be infringed by our technology. On May 5,
1998, the Opposition Division of the European Patent Office issued a provisional nonbinding opinion that the claims should be revoked. If the claims of the original European patent survive the
opposition or if an application relating to arrays issues in another country with claims as broad as the original European patent, we would be subject to infringement claims that could delay or
preclude sales of some or all of our anticipated diagnostic products.

We were and are currently involved in intellectual property litigation that was and is costly, time-consuming and may impact our competitive
position.

In July 2001, we entered into a settlement agreement with Motorola, Genometrix and MIT concluding the declaratory judgment action by us against
Motorola, Genometrix and MIT and Motorola's counterclaim against us. In connection with the settlement, we have secured a license from Motorola to certain claims of the '939 Patent. In exchange,
Nanogen paid the parties involved a total of $2.5 million in cash and $2.5 million in Nanogen common stock (equal to 416,666 shares based upon a per share price of $6.00, the fair market
value on the date of settlement). The settlement does not include any cross-licensing provisions of Nanogen technology to Motorola, Genometrix or MIT. Nanogen's lawsuit and Motorola's counterclaim
have now been dismissed.

In
November 2000, we filed a complaint against CombiMatrix Corp. ("CombiMatrix") and Dr. Donald Montgomery in the United States District Court for the Southern District
of California. Dr. Montgomery is a former Nanogen employee now affiliated with CombiMatrix. The Nanogen complaint alleges that the naming of Dr. Montgomery as the sole inventor on U.S.
Patent No. 6,093,302, entitled "Electrochemical Solid Phase Synthesis" (the "'302 patent"), and assignment of the '302 patent to CombiMatrix were incorrect and that the invention was made by
Nanogen employees. The complaint also alleges that inventions disclosed in the patent were Nanogen trade

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secrets and that CombiMatrix and Dr. Montgomery misappropriated these trade secrets by their actions, including publishing those trade secrets in patent applications. Nanogen's complaint seeks
correction of inventorship, assignment of rights in the patent to Nanogen, an injunction preventing disclosure of trade secrets and damages for trade secret misappropriation.

In
December 2000, CombiMatrix and Dr. Montgomery filed a motion to dismiss Nanogen's complaint. In January 2001, the motion was denied as to all claims except a
claim for conversion, as to which the motion was granted without prejudice. We elected not to amend our complaint as to the conversion claim. On March 9, 2001, CombiMatrix and
Dr. Montgomery answered Nanogen's complaint, asserted various affirmative defenses and filed a counterclaim for breach of contract against Nanogen for unspecified damages allegedly arising from
the filing of the complaint at a time when CombiMatrix had announced its intent to make an initial public offering of its shares. The counterclaim asserts that Nanogen, by filing its complaint,
breached a settlement agreement entered into between Nanogen and Dr. Montgomery in 1995. On May 14, 2001, Nanogen filed a motion to dismiss CombiMatrix's counterclaim, which was denied
on July 27, 2001. Discovery is currently ongoing.

No
assurances can be given that we will prevail in the lawsuit or that we can successfully defend ourselves against the counterclaim. We are expending considerable financial resources
and managerial efforts prosecuting the lawsuit and defending against Dr. Montgomery's and CombiMatrix's counterclaim. We may not prevail in the action, which could have a material adverse
effect on us.

The regulatory approval process is expensive, time consuming, uncertain and may prevent us from obtaining required approvals for the commercialization
of our products.

We anticipate that the manufacturing, labeling, distribution and marketing of any potential diagnostic products we may develop will be subject to regulation in
the U.S. and other countries. These regulations could subject us to several problems such as:



In
the U.S., the Food and Drug Administration, or FDA, regulates as medical devices most test systems, kits, and in vitro reagents that are marketed for human diagnostic use. Pursuant
to the Federal Food, Drug, and Cosmetic Act, the FDA regulates the preclinical and clinical testing, design, safety, effectiveness, manufacture, labeling, distribution and promotion of medical
devices. We will not be able to commence marketing or commercial sales in the U.S. of these products until we receive clearance or approval from the FDA, which can be a lengthy, expensive and
uncertain process. We have not applied for FDA or other regulatory approvals with respect to any of our products under development. We may experience difficulties that could delay or prevent the
successful development, introduction and marketing of proposed products. Regulatory clearance or approval of any proposed products may not be granted by the FDA or foreign regulatory authorities on a
timely basis, if at all.

Noncompliance
with applicable FDA requirements can result in:



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The
FDA also has the authority to request the recall, repair, replacement or refund of the cost of any regulated device that may eventually be manufactured or distributed by us. Any
devices manufactured or distributed by us pursuant to FDA clearance or approvals are subject to thorough and continuing regulation by the FDA and certain state agencies, including the California
Department of Health Services.

We depend on suppliers for materials that could impair our ability to manufacture our products.

Outside vendors provide key components and raw materials used by us and Hitachi in the manufacture of our products. Although we believe that alternative
sources for these components and raw materials are available, any supply interruption in a limited or sole source component or raw material would harm our and Hitachi's ability to manufacture our
products until a new source of supply is identified and qualified. In addition, an uncorrected defect or supplier's variation in a component or raw material, either unknown to us or Hitachi or
incompatible with our or Hitachi's manufacturing processes, could harm our or Hitachi's ability to manufacture products. We or Hitachi may not be able to find a sufficient alternative supplier in a
reasonable time period, or on commercially reasonable terms, if at all. If we or Hitachi fail to obtain a supplier for the manufacture of components of our potential products, we may be forced to
curtail or cease operations.

We may not be able to manufacture products on a commercial scale.

We and Hitachi rely on subcontractors to manufacture the limited quantities of microchips and other components we require for use by and sale to our customers,
as well as for internal and collaborative purposes.

Manufacturing,
supply and quality control problems may arise as we or Hitachi either alone, together or with subcontractors, attempt to scale up manufacturing procedures. We or
Hitachi may not be able to scale-up in a timely manner or at a commercially reasonable cost. Problems could lead to delays or pose a threat to the ultimate commercialization of our
products and cause us to fail.

We
or Hitachi or any of our contract manufacturers could encounter manufacturing difficulties, including:



Our
manufacturing facilities and those of Hitachi and any other of our contract manufacturers are or will be subject to periodic regulatory inspections by the FDA and other federal,
state and international regulatory agencies and these facilities are or may become subject to Quality System Regulation, or QSR, requirements of the FDA. If we, Hitachi or our third-party
manufacturers, fail to maintain facilities in accordance with QSR regulations, other international quality standards or other regulatory requirements then the manufacture process could be suspended or
terminated which would harm us.

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Lead times for materials, components and our products vary significantly which could lead to excess inventory levels as well as shortages of critical
components or products if our supply forecasts are inaccurate.

We anticipate that our products will be manufactured based on forecasted demand and will seek to purchase components and materials in anticipation of the
actual receipt of purchase orders for our products from customers. Lead times for materials, components and our products vary significantly and depend on factors such as the business practices of each
specific supplier and the terms of the particular contracts, as well as the overall market demand for such materials, components and products at any given time. If the forecasts are inaccurate, we
could experience fluctuations in excess inventory of our products, or shortages of critical components or products, either of which could cause our business to suffer.

We currently rely on one manufacturer of our Workstation which may delay the manufacture and shipment of our products to customers.

We have signed an exclusive manufacturing agreement with Hitachi to manufacture our NanoChip® Workstation and a collaboration agreement to
exclusively manufacture certain of our other products to be developed, subject to certain terms and conditions in each agreement. We have retained exclusive rights pursuant to each agreement to
manufacture the NanoChip® cartridges. Pursuant to the manufacturing agreement and the collaboration agreement, each party is obligated to provide the other with certain notice periods if
such party determines to curtail or terminate the manufacturing relationship. Nevertheless, while alternative manufacturers of our Workstation and other products currently exist, a lengthy process
would be required to negotiate and begin work under a manufacturing agreement with a new manufacturer which could disrupt our manufacturing process and harm our business.

Energy shortages may adversely impact our operations.

California has been experiencing shortages of electrical power and other energy sources. This condition has periodically resulted in rolling brownouts, or the
temporary and generally unannounced loss of the primary electrical power source. Our laboratory facility in San Diego is powered by electricity. We do not have secondary electrical power sources to
mitigate the impacts of temporary or longer-term electrical outages. It is not anticipated that the power shortages will abate soon, and therefore, our operating facilities may experience
brown-outs, black-outs, or other consequences of the shortage, and may be subject to usage restrictions or other energy consumption regulations that could adversely impact or
disrupt our research and development, manufacturing and other activities.

The number of our sales and marketing employees may not result in corresponding numbers of sales or placements of the NanoChip® System.

At September 30, 2001, we had 29 employees in our sales and marketing group. In addition, in July 2000, we incorporated a subsidiary, Nanogen
Europe B.V. in The Netherlands as our European sales office. At September 30, 2001, this office employed 7 European-based sales executives and support personnel in the United Kingdom, Germany,
The Netherlands and Denmark.

Developing,
training and monitoring this sales and marketing force has required and will further require capital and time expenditures by Nanogen and certain of its employees. The
size of our sales and marketing force may not result in corresponding numbers of sales or placements of the NanoChip® System nor increased product revenues associated with such sales or
placements. Nanogen may be required to increase or decrease the size of this sales and marketing force as deemed necessary and such increases or decreases in staff will require additional capital and
time expenditures by Nanogen and its employees.

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Failure to expand our international sales as we intend would reduce our ability to become profitable.

We expect that a portion of our sales will be made outside the United States. A successful international effort will require us to develop relationships with
international customers and partners. We may not be able to identify, attract or retain suitable international customers and distribution partners. As a result, we may be unsuccessful in our
international expansion efforts. Furthermore, expansion into international markets will require us to continue to establish and expand foreign sales and marketing efforts, hire additional sales and
marketing personnel and maintain good relations with our foreign customers and distribution partners.

International
operations involve a number of risks not typically present in domestic operations, including:



Our
international sales and marketing efforts will also be subject to the risks associated with the imposition of legislation and regulations relating to the import or export of high
technology products. We cannot predict whether tariffs or restrictions upon the importation or exportation of our products will be implemented by the United States or other countries.

We
may lose money when we exchange foreign currency received from international sales into US dollars. A portion of our business is expected to be conducted in currencies other than
the U.S. dollar. We recognize foreign currency gains or losses arising from our operations in the period incurred. As a result, currency fluctuations between the US dollar and the currencies in which
we do business will cause foreign currency transaction gains and losses. We cannot predict the effects of exchange rate fluctuations upon our future operating results because of the number of
currencies involved, the variability of currency exposure and the potential volatility of currency exchange rates. We currently do not engage in foreign exchange hedging transactions to manage our
foreign currency exposure.

If we fail to manage our growth, our business could be impaired.

We have experienced growth in the number of our employees and the scope of our operating and financial systems since December 31, 2000. This growth has
resulted in an increase in responsibilities for both existing and new management personnel. Our ability to manage this growth effectively will require us to continue to implement and improve our
operational, financial and management information
systems and to recruit, train, motivate and manage our employees. We may not be able to manage such growth and expansion, which would impair our business.

We may have significant product liability exposure.

We face an inherent business risk of exposure to product liability and other claims in the event that our technologies or products are alleged to have caused
harm. These risks are inherent in the

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testing, manufacturing and marketing of our products. We may not be able to obtain insurance for such potential liability on acceptable terms with adequate coverage, or at reasonable costs. Any
potential product liability claims could exceed the amount of our insurance coverage or may be excluded from coverage under the terms of the policy. Our insurance, once obtained, may not be renewed at
a cost and level of coverage comparable to that then in effect.

If we lose our key personnel or are unable to attract and retain additional personnel, we may not be able to pursue collaborations or develop our own
products.

We are highly dependent on the principal members of our scientific, manufacturing, marketing and management personnel, the loss of whose services might
significantly delay or prevent the achievement of our objectives. We face competition from other companies, academic institutions, government entities and other organizations in attracting and
retaining personnel.

Health care reform and restrictions on reimbursement may limit our returns on potential products.

Our ability to earn sufficient returns on our products will depend in part on the extent to which reimbursement for our products and related treatments will be
available from:



If
appropriate reimbursement cannot be obtained, we could be prevented from successfully commercializing our potential products.

There
are efforts by governmental and third party payors to contain or reduce the costs of health care through various means. We expect that there will continue to be a number of
legislative proposals to implement government controls. The announcement of proposals or reforms could impair our ability to raise capital. The adoption of proposals or reforms could impair our
business.

Additionally,
third party payors are increasingly challenging the price of medical products and services. If purchasers or users of our products are not able to obtain adequate
reimbursement for the cost of using our products, they may forego or reduce their use. Significant uncertainty exists as to the reimbursement status of newly approved health care products, and whether
adequate third party coverage will be available.

If ethical and other concerns surrounding the use of genetic information become widespread, we may have less demand for our products.

Genetic testing has raised ethical issues regarding confidentiality and the appropriate uses of the resulting information. For these reasons, governmental
authorities may call for limits on or regulation of the use of genetic testing or prohibit testing for genetic predisposition to certain conditions, particularly for those that have no known cure. Any
of these scenarios could reduce the potential markets for our products, which could seriously harm our business, financial condition and results of operations.

We use hazardous materials in our business. Any claims relating to improper handling, storage or disposal of these materials could be time consuming and
costly.

Our research and development processes involve the controlled storage, use and disposal of hazardous materials including biological hazardous materials and
radioactive compounds. We are

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subject to federal, state and local regulations governing the use, manufacture, storage, handling and disposal of materials and waste products. Although we believe that our safety procedures for
handling and disposing of these hazardous materials comply with the standards prescribed by law and regulation, the risk of accidental contamination or injury from hazardous materials cannot be
completely eliminated. In the event of an accident, we could be held liable for any damages that result, and any liability could exceed the limits or fall outside the coverage of our insurance. We may
not be able to maintain insurance on acceptable terms, or at all. We could be required to incur significant costs to comply with current or future environmental laws and regulations.

Our stock price could continue to be highly volatile and our stockholders may not be able to resell their shares at or above the price they paid for
them.

The market price of our common stock, like that of many other life sciences companies, has been highly volatile and is likely to continue to be highly
volatile. The following factors, among others, could have a significant impact on the market price of our common stock:



Our anti-takeover provisions could discourage potential takeover attempts and make attempts by stockholders to change management more
difficult.

The approval of two-thirds of our voting stock is required to approve some transactions and to take some stockholder actions, including the calling
of a special meeting of stockholders and the amendment of any of the anti-takeover provisions contained in our certificate of incorporation. Further, pursuant to the terms of our
stockholder rights plan adopted in November 1998, as amended, we have

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distributed a dividend of one right for each outstanding share of common stock. These rights will cause substantial dilution to the ownership of a person or group that attempts to acquire us on terms
not approved by our board of directors and may have the effect of deterring hostile takeover attempts.

If we make any acquisitions, we will incur a variety of costs and may never realize the anticipated benefits.

If appropriate opportunities become available, we may attempt to acquire businesses, technologies, services or products that we believe are a strategic fit
with our business. We currently have no commitments or agreements with respect to any material acquisitions. If we do undertake any transaction of this sort, the process of integrating an acquired
business, technology, service or product may result in operating difficulties and expenditures and may absorb significant management attention that would otherwise be available for ongoing development
of our business. Moreover, we may never realize the anticipated benefits of any acquisition. Future acquisitions could result in potentially dilutive issuances of equity securities, the incurrence of
debt, contingent liabilities and/or amortization expenses related to certain intangible assets, which could adversely affect our results of operations and financial condition.

Item 3. Quantitative and Qualitative Disclosures About Market Risk

Short-term investments.We invest our excess cash in short-term, interest-bearing
investment-grade securities that primarily are held for the duration of the term of the respective instrument. We have not utilized derivative financial instruments, derivative commodity instruments
or other market risk sensitive instruments, positions or transactions in any material fashion. Accordingly, we believe that, while the instruments we hold are subject to changes in the financial
standing of the issuer of such securities, we are not subject to any material risks arising from changes in interest rates, foreign currency exchange rates, commodity prices, equity prices or other
market changes that affect market risk sensitive instruments.

Foreign currency rate fluctuations.The functional currency for our Netherlands and German subsidiaries is the U.S.
dollar and euro, respectively. The German subsidiary's accounts are translated from the euro to the U.S. dollar using the current exchange rate in effect at the balance sheet date for balance sheet
accounts, and using the average exchange rate during the period for revenues and expense accounts. The effects of translation are recorded in accumulated other comprehensive income in the consolidated
financial statements included herein. In certain instances, our subsidiaries conduct business with customers and vendors in euros or in other local European currencies. Exchange gains and losses
arising from these transactions are recorded using the actual exchange rate differences on the date of the transaction. We have not taken any action to reduce our exposure to changes in foreign
currency exchange rates, such as options or futures contracts, with respect to transactions with our European customers and vendors. The net tangible assets of our subsidiaries, excluding intercompany
balances, is $6.4 million at September 30, 2001.

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PART IIOTHER INFORMATION

Item 1. Legal Proceedings

Please see discussion of legal proceedings at note 5 in the Notes to the Consolidated Financial Statements included elsewhere in this report.

Item 6. Exhibits and Reports on Form 8-K

(a)  Exhibits

|3.(ii)1 |  | Amended and Restated Bylaws of Nanogen, Inc.                                                                                                   
|------- |  | -----------------------------------------------------------------------------------------------------------------------------------------------
|10.1    |  | Second Amendment to Employment Agreement between Michael D. Moore and Nanogen, Inc., dated July 1, 2001                                        
|10.2    |  | Amended and Restated Employment Agreement between Howard C. Birndorf and Nanogen, Inc., dated as of June 3, 2001                               
|10.3    |  | Amended and Restated Employment Agreement between Kieran T. Gallahue and Nanogen, Inc., dated as of April 27, 2001                             
|10.4    |  | Amended and Restated Employment Agreement between Vera P. Pardee, Esq. and Nanogen, Inc., dated as of April 27, 2001                           
|10.5    |  | Amended and Restated Employment Agreement between Gerard A. Wills and Nanogen, Inc., dated as of April 27, 2001                                
|10.6(+) |  | Settlement Agreement between Motorola, Inc., Genometrix, Inc., the Massachusetts Institute of Technology and Nanogen, Inc., dated July 20, 2001
|10.7    |  | Nanogen, Inc. 1997 Stock Incentive Plan, as amended                                                                                            

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(b)  Reports
on Form 8-K

On
July 24, 2001, the Company filed an 8-K to report that the Company entered into a settlement agreement with Motorola, Inc. Genometrix, Inc. and the
Massachusetts Institute of Technology ("MIT") on July 20, 2001 concluding the declaratory judgement action by Nanogen against Motorola, Genometrix, and MIT and Motorola's counterclaim against
Nanogen. In connection with the settlement, the Company secured a license from Motorola to certain claims of the '939 Patent. In exchange, the Company made a one-time payment of
$2.5 million in cash and issued 416,666 shares of the Company's common stock (valued at approximately $2.5 million based upon a per share price of $6.00, the fair market value on the
date of settlement) to the parties involved. The settlement does not include any cross-licensing provisions of the Company's technology to Motorola, Genometrix or MIT. The lawsuit and the counterclaim
have now been dismissed.

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NANOGEN, INC.        SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned
thereunto duly authorized.

|     |  |                   |  | NANOGEN, INC.                                                                                                                        
|---- |  | ----------------- |  | -------------------------------------------------------------------------------------------------------------------------------------
|Date |  | November 13, 2001 |  | /s/ Howard C. BirndorfHoward C. Birndorf
Executive Chairman
(Principal Executive Officer)                                            
|Date |  | November 13, 2001 |  | /s/ Gerard A. WillsGerard A. Wills
Vice President, Chief Financial
Officer and Treasurer
(Principal Financial and Accounting
Officer)

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NANOGEN, INC.        EXHIBIT INDEX

|Exhibit No. |  | Description                                                                                                                                    
|----------- |  | -----------------------------------------------------------------------------------------------------------------------------------------------
|3.(ii)1     |  | Amended and Restated Bylaws of Nanogen, Inc.                                                                                                   
|10.1        |  | Second Amendment to Employment Agreement between Michael D. Moore and Nanogen, Inc., dated July 1, 2001                                        
|10.2        |  | Amended and Restated Employment Agreement between Howard C. Birndorf and Nanogen, Inc., dated as of June 3, 2001                               
|10.3        |  | Amended and Restated Employment Agreement between Kieran T. Gallahue and Nanogen, Inc., dated as of April 27, 2001                             
|10.4        |  | Amended and Restated Employment Agreement between Vera P. Pardee, Esq. and Nanogen, Inc., dated as of April 27, 2001                           
|10.5        |  | Amended and Restated Employment Agreement between Gerard A. Wills and Nanogen, Inc., dated as of April 27, 2001                                
|10.6(+)     |  | Settlement Agreement between Motorola, Inc., Genometrix, Inc., the Massachusetts Institute of Technology and Nanogen, Inc., dated July 20, 2001
|10.7        |  | Nanogen, Inc. 1997 Stock Incentive Plan, as amended                                                                                            

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