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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 June 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(State or other jurisdiction of
incorporation or organization)

33-0489621(I.R.S Employer Identification No.)10398 Pacific Center Court, San Diego, CA(Address of principal executive offices)

92121(Zip code)


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

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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 August 9, 2001, 21,426,999 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 June 30, 2001 and December 31, 2000                              |  | 3   
|                              |  | Consolidated Statements of Operations for the Three and Six Months ended June 30, 2001 and 2000 |  | 4   
|                              |  | Consolidated Statements of Cash Flows for the Six Months ended June 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           |  | 9   
|Item 3.                       |  | Quantitative and Qualitative Disclosures About Market Risk                                      |  | 23  
|PART II: OTHER INFORMATION    |  |                                                                                                
|Item 1.                       |  | Legal Proceedings                                                                               |  | 24  
|Item 2.                       |  | Changes in Securities                                                                           |  | 24  
|Item 4.                       |  | Submission of Matters to a Vote of Security Holders                                             |  | 24  
|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)

|                                                |                                                                                                                                                                           | June 30,
2001 |        | December 31,
2000 |  
|----------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------- | ------ | ----------------- | -
|
|ASSETS                                          |                                                                                                                                                                           |               |        |                   |  
|Current assets:                                 |                                                                                                                                                                           |               |        |                   |  
|                                                | Cash and cash equivalents                                                                                                                                                 |               | $      | 20,419            |  
|                                                | Short-term investments                                                                                                                                                    |               |        | 57,938            |  
|                                                | Accounts receivable                                                                                                                                                       |               |        | 1,413             |  
|                                                | Inventory                                                                                                                                                                 |               |        | 4,234             |  
|                                                | Other current assets                                                                                                                                                      |               |        | 3,332             |  
|                                                |                                                                                                                                                                           |               |        |                   |  
|Total current assets                            |                                                                                                                                                                           |               | 87,336 |                   |  
|Property and equipment, net                     |                                                                                                                                                                           |               | 5,444  |                   |  
|Acquired technology rights, net                 |                                                                                                                                                                           |               | 4,579  |                   |  
|Restricted cash                                 |                                                                                                                                                                           |               | 164    |                   |  
|Other assets                                    |                                                                                                                                                                           |               | 203    |                   |  
|                                                |                                                                                                                                                                           |               |        |                   |  
|                                                |                                                                                                                                                                           | $             | 97,726 |                   | $
|                                                |                                                                                                                                                                           |               |        |                   |  
|LIABILITIES AND STOCKHOLDERS' EQUITY            |                                                                                                                                                                           |               |        |                   |  
|Current liabilities:                            |                                                                                                                                                                           |               |        |                   |  
|                                                | Accounts payable                                                                                                                                                          |               | $      | 622               |  
|                                                | Accrued liabilities                                                                                                                                                       |               |        | 5,419             |  
|                                                | Deferred revenue                                                                                                                                                          |               |        | 151               |  
|                                                | Current portion of capital lease obligations                                                                                                                              |               |        | 1,514             |  
|                                                |                                                                                                                                                                           |               |        |                   |  
|Total current liabilities                       |                                                                                                                                                                           |               | 7,706  |                   |  
|Capital lease obligations, less current portion |                                                                                                                                                                           |               | 2,186  |                   |  
|Other long-term liabilites                      |                                                                                                                                                                           |               | 3,000  |                   |  
|                                                |                                                                                                                                                                           |               |        |                   |  
|Total long-term liabilities                     |                                                                                                                                                                           |               | 5,186  |                   |  
|Stockholders' equity:                           |                                                                                                                                                                           |               |        |                   |  
|                                                | Convertible preferred stock, $.001 par value, 5,000,000 shares authorized; no shares issued and outstanding at June 30, 2001 and December 31, 2000                        |               |        |                  |  
|                                                | Common stock, $.001 par value, 50,000,000 shares authorized; 21,057,583 and 20,913,151 shares issued and outstanding at June 30, 2001 and December 31, 2000, respectively |               |        | 21                |  
|                                                | Additional paid-in capital                                                                                                                                                |               |        | 194,198           |  
|                                                | Accumulated other comprehensive income                                                                                                                                    |               |        | 862               |  
|                                                | Deferred compensation                                                                                                                                                     |               |        | (175              | )
|                                                | Notes receivable from officers                                                                                                                                            |               |        | (1,131            | )
|                                                | Accumulated deficit                                                                                                                                                       |               |        | (108,941          | )
|                                                |                                                                                                                                                                           |               |        |                   |  
|Total stockholders' equity                      |                                                                                                                                                                           |               | 84,834 |                   |  
|                                                |                                                                                                                                                                           |               |        |                   |  
|                                                |                                                                                                                                                                           | $             | 97,726 |                   | $
|                                                |                                                                                                                                                                           |               |        |                   |  

See accompanying notes.

3

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NANOGEN, INC.        CONSOLIDATED STATEMENTS OF OPERATIONS        (unaudited)        (in thousands, except per share data)

|                                                                          |                                            | Three months ended June 30, |         | Six months ended June 30, |  
|------------------------------------------------------------------------- | ------------------------------------------ | --------------------------- | ------- | ------------------------- | -
|
|Revenues:                                                                 |                                            |                             |         |                           |  
|                                                                          | Sales                                      |                             | $       | 302                       |  
|                                                                          | Sponsored research                         |                             |         | 2,055                     |  
|                                                                          | Contract and grant revenue                 |                             |         | 358                       |  
|                                                                          |                                            |                             |         |                           |  
|Total revenues                                                            |                                            |                             | 2,715   |                           |  
|Operating expenses:                                                       |                                            |                             |         |                           |  
|                                                                          | Cost of sales                              |                             |         | 230                       |  
|                                                                          | Research and development                   |                             |         | 4,414                     |  
|                                                                          | Selling, general and administrative        |                             |         | 5,406                     |  
|                                                                          | Litigation and settlement of patent matter |                             |         | 5,511                     |  
|                                                                          |                                            |                             |         |                           |  
|Total operating expenses                                                  |                                            |                             | 15,561  |                           |  
|                                                                          |                                            |                             |         |                           |  
|Loss from operations                                                      |                                            |                             | (12,846 | )                         |  
|Interest income, net                                                      |                                            |                             | 1,092   |                           |  
|Gain (loss) on foreign currency transactions                              |                                            |                             | 4       |                           |  
|                                                                          |                                            |                             |         |                           |  
|Net loss                                                                  |                                            | $                           | (11,750 | )                         | $
|                                                                          |                                            |                             |         |                           |  
|Net loss per share  basic and diluted                                    |                                            | $                           | (0.56   | )                         | $
|                                                                          |                                            |                             |         |                           |  
|Number of shares used in computing net loss per share  basic and diluted |                                            |                             | 20,847  |                           |  
|                                                                          |                                            |                             |         |                           |  

See
accompanying notes.

4

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NANOGEN, INC.        CONSOLIDATED STATEMENTS OF CASH FLOWS        (unaudited)        (in thousands)

|                                                                     |                                                                             | Six months ended
June 30,                                                        |        
|-------------------------------------------------------------------- | --------------------------------------------------------------------------- | -------------------------------------------------------------------------------- | -------
|
|Operating activities:                                                |                                                                             |                                                                                  |        
|                                                                     | Net loss                                                                    |                                                                                  | $      
|                                                                     | Adjustments to reconcile net loss to net cash used in operating activities: |                                                                                  |        
|                                                                     | Accrual for settlement of litigation                                        |                                                                                  |        
|                                                                     | Depreciation and amortization                                               |                                                                                  |        
|                                                                     | Amortization related to short-term investments                              |                                                                                  |        
|                                                                     | Stock based compensation expense                                            |                                                                                  |        
|                                                                     | Interest capitalized on notes receivables from officers                     |                                                                                  |        
|                                                                     | Changes in operating assets and liabilities:                                |                                                                                  |        
|                                                                     |                                                                             | Accounts receivable                                                              |        
|                                                                     |                                                                             | Inventory                                                                        |        
|                                                                     |                                                                             | Other assets                                                                     |        
|                                                                     |                                                                             | Accounts payable                                                                 |        
|                                                                     |                                                                             | Accrued liabilities                                                              |        
|                                                                     |                                                                             | Deferred revenue                                                                 |        
|                                                                     |                                                                             |                                                                                  |        
|Net cash used in operating activities                                |                                                                             |                                                                                  | (17,065
|Investing activities:                                                |                                                                             |                                                                                  |        
|                                                                     | Purchase of short-term investments                                          |                                                                                  |        
|                                                                     | Purchase of equipment                                                       |                                                                                  |        
|                                                                     | Purchase of technology rights                                               |                                                                                  |        
|                                                                     |                                                                             |                                                                                  |        
|Net cash used in investing activities                                |                                                                             |                                                                                  | (17,582
|Financing activities:                                                |                                                                             |                                                                                  |        
|                                                                     | Principal payments on capital lease obligations                             |                                                                                  |        
|                                                                     | Issuance of common stock, net of repurchases                                |                                                                                  |        
|                                                                     | Note receivable payments from officers                                      |                                                                                  |        
|                                                                     |                                                                             |                                                                                  |        
|Net cash provided by (used in) financing activities                  |                                                                             |                                                                                  | (264   
|Net (decrease) increase in cash and cash equivalents                 |                                                                             |                                                                                  | (34,911
|Cash and cash equivalents at beginning of period                     |                                                                             |                                                                                  | 55,330 
|                                                                     |                                                                             |                                                                                  |        
|Cash and cash equivalents at end of period                           |                                                                             | $                                                                                | 20,419 
|                                                                     |                                                                             |                                                                                  |        
|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                                        |        
|                                                                     |                                                                             |                                                                                  |        
|                                                                     |                                                                             | 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)        June 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 June 30, 2001, consolidated statements of operations for the three and six months ended June 30, 2001 and 2000, and the consolidated statements of cash flows for the six months ended
June 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 six months ended June 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 per share is computed by dividing the net income for the period by the weighted average number of common shares outstanding during the period and dilutive potential common shares
outstanding. 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 six months ended June 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.

2. Inventory

Inventory consists of the following (in thousands):

June 30,
2001

December 31,
2000Raw materials

$
705

$
288Work in process


1,075


491Finished goods


2,454


1,510$
4,234

$
2,289


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

6

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The Company's manufacturing agreement with Hitachi, Ltd. ("Hitachi") requires that the Company provide annual purchase commitments to Hitachi for NanoChip
Molecular Biology Workstations. As of June 30, 2001, the Company has commitments to purchase approximately $5.4 million in NanoChip Molecular Biology 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 June 30,

Six months ended June 30,2001

2000

2001

2000Comprehensive loss:Net unrealized gain

$
36

$


$
862

$
Net loss


(11,750
)

(4,113
)

(18,029
)

(7,791
)Comprehensive loss

$
(11,714
)
$
(4,113
)
$
(17,167
)
$
(7,791
)


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 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 June 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 which was received in the fourth quarter of 1999.

Revenue
is primarily recognized under these agreements as expenses are incurred, and totaled $1.8 million and $3.9 million for the three and six months ended
June 30, 2001, respectively, and $1.7 million and $3.6 million for the three and six months ended June 30, 2000, respectively. Funding received in advance of incurred
expenses is recorded as deferred revenue until the expenses are incurred, and totaled none and $123,000 at June 30, 2001 and December 31, 2000, respectively.

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 funding for the operations of the new company and has contributed intellectual property in the form of eighteen patents. In addition, Nanogen Recognomics will own
several patent applications filed jointly by the Company and Aventis. The Company has licensed certain aspects of its

7

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NanoChip technology to the new company and will 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 $9.83.

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 some claims of the
'939 Patent. In exchange, the Company will make a one-time payment of $2.5 million in cash and issue 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. As of June 30, 2001, these amounts have been accrued for in the Company's
financial statements.

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.

On
December 15, 2000, CombiMatrix and Dr. Montgomery filed a motion to dismiss the Company's complaint. On January 29, 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.

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 may have to expend 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.

8

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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 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 June 30, 2001, had an accumulated deficit of $108.9 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 six months ended June 30, 2001 sales totaled $302,000 and $531,000, respectively,
compared to $164,000 for the three and six months ended June 30, 2000. Sales revenue during the three months ended June 30, 2001 includes the sale of two NanoChip Molecular
Biology Workstations through outright sales transactions where the title of the instrument passed to the customer as well as sales of NanoChip Cartridges. For the six months ended
June 30, 2001, sales revenue includes sales of three NanoChip Molecular Biology Workstations in addition to sales of NanoChip Cartridges. Sales revenue for the three
and six months ended June 30, 2000 was comprised of the sale of our first NanoChip Molecular Biology Workstation as well as our first 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 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.

9

---

For the three and six months ended June 30, 2001 revenues from sponsored research totaled $2.1 million and $4.4 million, respectively, compared to
$1.7 million and $3.6 million for the three and six months ended June 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 six months ended
June 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.
Sponsored research revenue recognized during these periods in 2001 also includes revenue earned in connection with our development program entered into in July 2000 with Hitachi. Additionally,
sponsored research revenue recognized during the three and six months ended June 30, 2001 includes the sale of two NanoChip Molecular Biology Workstations to one of the Aventis
programs. Sponsored research revenue recognized during the three and six months ended June 30, 2000, was earned in connection with the research and development agreements entered into in
December 1998 and September 1999 with Aventis.

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 six months ended June 30, 2001 were 23.8% and 24.7%,
respectively, and were impacted by the sale of a NanoChip Molecular Biology Workstation to a distributor 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 and six months ended June 30, 2000, gross margins were 92.7% and were impacted by the sale of one NanoChip
Molecular Biology 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 six months ended June 30, 2001 research and development
expenses totaled $4.4 million and $9.2 million, respectively, compared to $4.5 million and $8.8 million for the three and six months ended June 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, lab supplies, consulting, travel, facilities, and other expenditures associated with our research and product development activities.
Research and development spending may increase over the next several years as our research and product development efforts continue.

Selling, General and Administrative Expenses.For the three and six months ended June 30, 2001 selling, general
and administrative expenses totaled $5.4 million and $10.2 million, respectively, compared to $3.3 million and $5.6 million for the three and six months ended
June 30, 2000, respectively. The increase is primarily due to costs associated with the expansion and development of our sales and marketing organization. Selling, general and administrative
expenses are expected to continue at this 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 six months ended June 30, 2001 litigation and
settlement of a patent matter totaled $5.5 million and $6.3 million, respectively. There were no comparable expenses for the three and six months ended June 30, 2000. Costs
incurred during

10

---

the three and six month period ended June 30, 2001 primarily consist of the settlement fee of $5 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 agreed to pay a total of
$5 million to the parties in the form of $2.5 million in cash and $2.5 million in our common stock (approximately 416,666 shares).

Interest Income, Net.For the three and six months ended June 30, 2001 net interest income totaled
$1.1 million and $2.4 million, respectively, compared to $1.4 million and $1.9 million for the three and six months ended June 30, 2000, respectively. The decrease
in net interest income for the quarter is a result of lower average cash balances during the three months ended June 30, 2001 compared to the same period in 2000. Cash proceeds received in
conjunction with the follow-on offering of our common stock in March 2000 resulted in an increase in net interest income for the six months ended June 30, 2001 when compared
to the same period in 2000.

Liquidity and Capital Resources

At June 30, 2001, we had $78.4 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 six months ended June 30, 2001.

Net
cash used in operating activities was $17.1 million and $11.5 million for the six months ended June 30, 2001 and 2000, respectively. Cash used for operations
during the six months ended June 30, 2001 was primarily related to costs associated with our expanded sales and marketing organization as the launch of our initial products progresses, an
increase of $1.9 million in inventory pursuant to our manufacturing arrangement with Hitachi, Ltd., $1.3 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.

We
fund most of our equipment acquisitions and leasehold improvements through capital leasing facilities. During the first six months of 2001, we financed approximately $983,000 of
capital equipment, compared to approximately $391,000 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. ("Hitachi") requires that we provide annual purchase commitments to Hitachi for NanoChip Molecular Biology
Workstations. As of June 30, 2001, we have commitments to purchase approximately $5.4 million in NanoChip Molecular Biology 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.

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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 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.

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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, Ltd. 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.

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 six months ended June 30, 2001. From our inception to June 30, 2001, we have incurred cumulative net losses totaling approximately $108.9 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:



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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:



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.

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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.

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.

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

In April 2000, we filed a complaint for declaratory judgment against Motorola, Beckman and MIT in the United States District Court for the Southern
District of California. Prior to the filing of the complaint, the parties had been involved in licensing discussions concerning U.S. Patent No. 5,693,939 entitled "Optical and Electrical
Methods and Apparatus For Molecule Detection" (the '939 patent") which was licensed by MIT to Beckman in 1993 and to Genometrix, Inc. or Genometrix in 1994. Genometrix subsequently granted its
sublicensing rights to Motorola in 1999. The inventions claimed in the '939 patent were made with United States government funding through a grant from the Department of the Air Force. The complaint
sought, among other things, a declaration that we are entitled to a license to the government funded '939 patent and, in the event we proceed to take a license, that we are not required to obtain a
license from both Motorola and Beckman. Alternatively, the complaint sought a declaratory judgment that the claims of the '939 patent were invalid and not infringed by us.

In
May 2000, we reached a settlement with Beckman and dismissed Beckman from the lawsuit without prejudice. In connection with the settlement, we secured a license to the '939
patent from Beckman. The action continued against Motorola and MIT. Motorola filed a counterclaim against us in May 2000, claiming infringement of the '939 patent and seeking monetary damages
and injunctive relief. Motorola's counterclaim asserted that it had exclusive rights to certain claims in the '939 patent. In October 2000, our motion for leave to amend the complaint to add
Genometrix as a defendant was granted.

In
July 2001, we reached a settlement with Motorola, Genometrix and MIT. Pursuant to the settlement, Nanogen secured from Motorola a license to and freedom to operate under
Claims 16 and 39 of the '939 Patent. In exchange, Nanogen agreed to pay the parties involved a total of $2.5 million in cash and $2.5 million in Nanogen common stock. 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. We have expended considerable
financial resources and managerial efforts prosecuting, defending and settling the lawsuit and counterclaim.

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 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.

On
December 15, 2000, CombiMatrix and Dr. Montgomery filed a motion to dismiss Nanogen's complaint. On January 29, 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.

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No assurances can be given that we will prevail in the lawsuit or that we can successfully defend ourselves against the counterclaim. We will have to expend 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:



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

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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.

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

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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 increase in the number of our sales and marketing employees may not result in increases in sales or placements of the NanoChip System.

We increased the number of employees in our sales and marketing group from 26 at December 31, 2000 to 34 at June 30, 2001. In addition, in
July 2000, we incorporated a subsidiary, Nanogen Europe B.V. in The Netherlands as our European sales office. At June 30, 2001, this office employed 8 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 increased 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.

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:



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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 expect to continue to experience growth in the number of our employees and the scope of our operating and financial systems. This growth has resulted in an
increase in responsibilities for both existing and new management personnel. Our ability to manage 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 our 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 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.

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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 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.

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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 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

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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

We invest our excess cash in short-term, interest-bearing investment-grade securities that 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.

The
functional currency for our Netherlands subsidiary is the U.S. dollar. In certain instances, our subsidiary conducts its business with customers and vendors in Euros or other in
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 subsidiary, excluding intercompany balances, is $852,000 at June 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 2. Changes in Securities

(c) Pursuant to agreements entered into in June 2001, we issued a warrant to purchase 315,863 shares of our common stock to Aventis Research and
Technologies, GmbH, at a price of $9.83. The warrant has a five year term and will expire in July 2006. Based in part upon the institutional nature of Aventis and the representations of
Aventis, the warrant was issued pursuant to the exemption from registration provided by Section 4(2) of the Securities Act of 1933. See Note 4 in the Notes to Consolidated Financial
Statements for a description of the Aventis agreements.

Item 4. Submission of Matters to a Vote of Security Holders

(a) On June 13, 2001, the Registrant held its Annual Meeting of Stockholders.

(b)
As listed below, all of management's nominees for directors were elected at the meeting:

Name of Nominee

No. of Votes For

No. of Votes WithheldVal Buonaiuto

18,357,252

307,314David G. Ludvigson

18,394,887

269,679Vance R. White, Ph.D.

18,392,659

271,907




|    |  |     |  |                                                                                                                                                                                                                                                                                     
|--- |  | --- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|(c) |  | (1) |  | The proposal to amend the Company's 1997 Stock Incentive Plan to increase the number of shares reserved for issuance thereunder by 1,500,000 was approved with 9,629,743 shares voting in favor, 2,139,036 voting against,
31,990 shares abstaining, and 6,863,797 broker non-votes.
|    |  |     |  |                                                                                                                                                                                                                                                                                     
|    |  | (2) |  | The proposal to amend the Company's Employee Stock Purchase Plan to increase the number of shares reserved for issuance thereunder by 150,000 was approved with 11,376,587 shares voting in favor 389,849 voting against,
34,333 shares abstaining, and 6,863,797 broker non-votes. 
|    |  |     |  |                                                                                                                                                                                                                                                                                     
|    |  | (3) |  | The appointment of Ernst & Young LLP as independent auditors of the Company for the fiscal year ending December 31, 2001 was ratified with 18,602,029 shares voting in favor, 41,842 voting against, and 20,695
shares abstaining.                                                  

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Item 6. Exhibits and Reports on Form 8-K



|10.1       |  | Employment Agreement between Gerard A. Wills and Nanogen, Inc., dated April 26, 2001                                                                                                                
|---------- |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|10.2       |  | Employment Agreement between V. Randy White and Nanogen, Inc. dated June 4, 2001                                                                                                                    
|10.3(+)    |  | Cooperation and Shareholders' Agreement among Aventis Research & Technologies GmbH & Co. KG ("Aventis R&T"), Nanogen, Inc. and Nanogen Recognomics GmbH ("Nanogen Recognomics"), dated June 29, 2001
|10.4(+)    |  | Contribution Agreement among Aventis R&T, Nanogen, Inc. and Nanogen Recognomics, dated June 27, 2001                                                                                                
|10.5       |  | Nanogen, Inc. 1997 Stock Incentive Plan, as amended                                                                                                                                                 
|10.6(+)(+) |  | Nanogen, Inc. Employee Stock Purchase Plan, as amended                                                                                                                                              

---

|(+)    |  | Confidential treatment has been requested for certain portions of this agreement.                                                  
|------ |  | -----------------------------------------------------------------------------------------------------------------------------------
|(+)(+) |  | Incorporated by reference to Exhibit 99.1 filed as part of Nanogen, Inc.'s Registration Statement on Form S-8 (Reg. No. 333-63426).





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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 August 13, 2001 |  | /s/ Howard C. BirndorfHoward C. Birndorf
Chairman of the Board
(Principal Executive Officer)                                         
|Date August 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                                                                                                                                                                                         
|----------- |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|10.1        |  | Employment Agreement between Gerard A. Wills and Nanogen, Inc., dated April 26, 2001                                                                                                                
|10.2        |  | Employment Agreement between V. Randy White and Nanogen, Inc. dated June 4, 2001                                                                                                                    
|10.3(+)     |  | Cooperation and Shareholders' Agreement among Aventis Research & Technologies GmbH & Co. KG ("Aventis R&T"), Nanogen, Inc. and Nanogen Recognomics GmbH ("Nanogen Recognomics"), dated June 29, 2001
|10.4(+)     |  | Contribution Agreement among Aventis R&T, Nanogen, Inc. and Nanogen Recognomics, dated June 27, 2001                                                                                                
|10.5        |  | Nanogen, Inc. 1997 Stock Incentive Plan, as amended                                                                                                                                                 
|10.6(+)(+)  |  | Nanogen, Inc. Employee Stock Purchase Plan, as amended                                                                                                                                              

---

|(+)    |  | Confidential treatment has been requested for certain portions of this agreement.                                                  
|------ |  | -----------------------------------------------------------------------------------------------------------------------------------
|(+)(+) |  | Incorporated by reference to Exhibit 99.1 filed as part of Nanogen, Inc.'s Registration Statement on Form S-8 (Reg. No. 333-63426).

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