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SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549



FORM 10-Q



Quarterly report pursuant to Section 13 or 15 (d)

of the Securities Exchange
Act of 1934



|For the Quarter Ended September 30, 2003 |  | Commission File No. 0-20948
|---------------------------------------- |  | ---------------------------



AUTOIMMUNE INC.

(Exact Name of Registrant as Specified in its Charter)



|Delaware                 |  | 13-348-9062                         
|------------------------ |  | ------------------------------------
|(State of Incorporation) |  | (I.R.S. Employer Identification No.)



1199 Madia Street,
Pasadena, CA 91103

(Address of Principal Executive Offices)



(626) 792-1235

(Registrants Telephone No., including Area Code)



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



Yes x         No ̈



Indicate by check mark
whether the registrant is an accelerated filer (as defined in Rule 12b-2 of the Exchange Act).



Yes ̈No x



Number
of shares outstanding of the registrants Common Stock as of October 31, 2003:



|Common Stock, par value $.01 |  | 16,919,623 shares outstanding
|---------------------------- |  | -----------------------------



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##### Table of Contents

AUTOIMMUNE INC.



QUARTER ENDED SEPTEMBER 30, 2003



TABLE
OF CONTENTS



|PART IFINANCIAL INFORMATION                                                                                                                                             |  | Page Number
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |  | -----------
|Item 1    Financial Statements (Unaudited)                                                                                                                              |  |            
|                                                                                                                                                                         | 
|Balance Sheet December 31, 2002 and September 30, 2003                                                                                                                   |  | 2          
|                                                                                                                                                                         | 
|Statement of Operations for the three and nine months ended September 30, 2002 and 2003 and for the period from inception (September 9, 1988) through September 30, 2003 |  | 3          
|                                                                                                                                                                         | 
|Statement of Cash Flows for the nine months ended September 30, 2002 and 2003 and for the period from inception (September 9, 1988) through September 30, 2003.          |  | 4          
|                                                                                                                                                                         | 
|Notes to the Unaudited Financial Statements                                                                                                                              |  | 5          
|                                                                                                                                                                         | 
|Item 2    Managements Discussion and Analysis of Financial Condition and Results of Operations                                                                         |  | 8          
|                                                                                                                                                                         | 
|Item 3    Quantitative and Qualitative Disclosures about Market Risk                                                                                                    |  | 11         
|                                                                                                                                                                         | 
|Item 4    Controls and Procedures                                                                                                                                       |  | 11         
|                                                                                                                                                                         | 
|PART IIOTHER INFORMATION                                                                                                                                                |  |            
|                                                                                                                                                                         | 
|Item 6(a)Exhibits                                                                                                                                                       |  | 12         
|                                                                                                                                                                         | 
|Item 6(b)Reports on Form 8-K                                                                                                                                            |  | 12         
|                                                                                                                                                                         | 
|Signatures                                                                                                                                                               |  | 13         



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##### Table of Contents

PART 1FINANCIAL INFORMATION



ITEM 1.    FINANCIAL STATEMENTS



AUTOIMMUNE INC.

(A development stage company)

BALANCE SHEET

(Unaudited)



|                                                                                                                                                 |  | December 31,2002 |              |   | September 30, 2003 |  
|------------------------------------------------------------------------------------------------------------------------------------------------ |  | ---------------- | ------------ | - | ------------------ | -
|ASSETS                                                                                                                                           |  |                  |              |   |                    |  
|Current assets:                                                                                                                                  |  |                  |              |   |                    |  
|Cash and cash equivalents                                                                                                                        |  | $                | 5,033,000    |   |                    | $
|Marketable securities                                                                                                                            |  |                  | 4,985,000    |   |                    |  
|Interest receivable                                                                                                                              |  |                  |             |   |                    |  
|Prepaid expenses and other current assets                                                                                                        |  |                  | 81,000       |   |                    |  
|                                                                                                                                                 |  |                  |              |   |                    |  
|Total current assets                                                                                                                             |  |                  | 10,099,000   |   |                    |  
|Long term marketable securities                                                                                                                  |  |                  |             |   |                    |  
|Other assets                                                                                                                                     |  |                  |             |   |                    |  
|                                                                                                                                                 |  |                  |              |   |                    |  
|                                                                                                                                                 |  | $                | 10,099,000   |   |                    | $
|                                                                                                                                                 |  |                  |              |   |                    |  
|LIABILITIES AND STOCKHOLDERS EQUITY                                                                                                             |  |                  |              |   |                    |  
|Current liabilities:                                                                                                                             |  |                  |              |   |                    |  
|Accounts payable                                                                                                                                 |  | $                | 42,000       |   |                    | $
|Accrued professional fees                                                                                                                        |  |                  | 145,000      |   |                    |  
|                                                                                                                                                 |  |                  |              |   |                    |  
|Total current liabilities                                                                                                                        |  |                  | 187,000      |   |                    |  
|                                                                                                                                                 |  |                  |              |   |                    |  
|Stockholders equity:                                                                                                                            |  |                  |              |   |                    |  
|Common stock, $.01 par value; 25,000,000 shares authorized; 16,919,623 shares issued and outstanding at December 31, 2002 and
September 30, 2003 |  |                  | 169,000      |   |                    |  
|Additional paid-in capital                                                                                                                       |  |                  | 118,102,000  |   |                    |  
|Deficit accumulated during the development stage                                                                                                 |  |                  | (108,363,000 | ) |                    |  
|Accumulated other comprehensive income                                                                                                           |  |                  | 4,000        |   |                    |  
|                                                                                                                                                 |  |                  |              |   |                    |  
|Total stockholders equity                                                                                                                       |  |                  | 9,912,000    |   |                    |  
|                                                                                                                                                 |  |                  |              |   |                    |  
|                                                                                                                                                 |  | $                | 10,099,000   |   |                    | $
|                                                                                                                                                 |  |                  |              |   |                    |  



The accompanying notes
are an integral part of these financial statements.





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AUTOIMMUNE INC.

(A development stage company)

STATEMENT OF OPERATIONS

(Unaudited)



|                                                                |  | Three months ended |            |   | Nine months ended |   |            | Period frominception(September 9,1988) throughSeptember 30, 2003 | 
|--------------------------------------------------------------- |  | ------------------ | ---------- | - | ----------------- | - | ---------- | ---------------------------------------------------------------- | 
|                                                                |  | September 30,2002  |            |   | September 30,2003 |   |            | September 30,2002                                                | 
|Revenue:                                                        |  |                    |            |   |                   |   |            |                                                                  | 
|License rights                                                  |  | $                  | 18,000     |   |                   | $ | 25,000     |                                                                  | 
|Option fees                                                     |  |                    |           |   |                   |   |           |                                                                  | 
|Research and development revenue under collaborative agreements |  |                    |           |   |                   |   |           |                                                                  | 
|                                                                |  |                    |            |   |                   |   |            |                                                                  | 
|Total revenues                                                  |  |                    | 18,000     |   |                   |   | 25,000     |                                                                  | 
|                                                                |  |                    |            |   |                   |   |            |                                                                  | 
|Costs and expenses:                                             |  |                    |            |   |                   |   |            |                                                                  | 
|Research and development:                                       |  |                    |            |   |                   |   |            |                                                                  | 
|Related party                                                   |  |                    | 16,000     |   |                   |   | 15,000     |                                                                  | 
|All other                                                       |  |                    | 195,000    |   |                   |   | 55,000     |                                                                  | 
|General and administrative                                      |  |                    | 100,000    |   |                   |   | 114,000    |                                                                  | 
|                                                                |  |                    |            |   |                   |   |            |                                                                  | 
|Total costs and expenses                                        |  |                    | 311,000    |   |                   |   | 184,000    |                                                                  | 
|                                                                |  |                    |            |   |                   |   |            |                                                                  | 
|Total operating income (loss)                                   |  |                    | (293,000   | ) |                   |   | (159,000   | )                                                                | 
|                                                                |  |                    |            |   |                   |   |            |                                                                  | 
|Interest income                                                 |  |                    | 48,000     |   |                   |   | 29,000     |                                                                  | 
|Interest expense                                                |  |                    |           |   |                   |   |           |                                                                  | 
|Equity in net loss of unconsolidated affiliate                  |  |                    |           |   |                   |   | (25,000    | )                                                                | 
|Other expense                                                   |  |                    |           |   |                   |   |           |                                                                  | 
|                                                                |  |                    |            |   |                   |   |            |                                                                  | 
|Net income (loss)                                               |  | $                  | (245,000   | ) |                   | $ | (155,000   | )                                                                | 
|                                                                |  |                    |            |   |                   |   |            |                                                                  | 
|Net income (loss) per share-basic                               |  | $                  | (0.01      | ) |                   | $ | (0.01      | )                                                                | 
|                                                                |  |                    |            |   |                   |   |            |                                                                  | 
|Net income (loss) per share-diluted                             |  | $                  | (0.01      | ) |                   | $ | (0.01      | )                                                                | 
|                                                                |  |                    |            |   |                   |   |            |                                                                  | 
|Weighted average common shares outstanding-basic                |  |                    | 16,919,623 |   |                   |   | 16,919,623 |                                                                  | 
|                                                                |  |                    |            |   |                   |   |            |                                                                  | 
|Weighted average common shares outstanding-diluted              |  |                    | 16,919,623 |   |                   |   | 16,919,623 |                                                                  | 
|                                                                |  |                    |            |   |                   |   |            |                                                                  | 



The accompanying notes
are an integral part of these financial statements.



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AUTOIMMUNE INC.

(A development stage company)

STATEMENT OF CASH FLOWS

Increase (Decrease) in Cash and Cash Equivalents

(Unaudited)



|                                                                                                                   |  | Nine months ended |            |   | Period frominception(September 9,1988) throughSeptember 30,2003 |  
|------------------------------------------------------------------------------------------------------------------ |  | ----------------- | ---------- | - | --------------------------------------------------------------- | -
|                                                                                                                   |  | September 30,2002 |            |   | September 30, 2003                                              |  
|Cash flows from operating activities:                                                                              |  |                   |            |   |                                                                 |  
|Net income (loss)                                                                                                  |  | $                 | (638,000   | ) |                                                                 | $
|Adjustment to reconcile net loss to net cash used by operating activities:                                         |  |                   |            |   |                                                                 |  
|Interest expense related to demand notes converted into Series A mandatorily redeemable covertible preferred stock |  |                   |           |   |                                                                 |  
|Patent costs paid with junior convertible preferred and common stock                                               |  |                   |           |   |                                                                 |  
|Valuation of warrants issued in conjunction with license revenue                                                   |  |                   |           |   |                                                                 |  
|Depreciation and amortization                                                                                      |  |                   |           |   |                                                                 |  
|Loss on sale/disposal of fixed assets                                                                              |  |                   |           |   |                                                                 |  
|Decrease in capitalized patent costs                                                                               |  |                   |           |   |                                                                 |  
|Impairment of investment valuation                                                                                 |  |                   |           |   |                                                                 |  
|Equity in net loss of unconsolidated affiliate                                                                     |  |                   |           |   |                                                                 |  
|(Increase) decrease in interest receivable                                                                         |  |                   |           |   |                                                                 |  
|(Increase) decrease in prepaid expenses and other current assets                                                   |  |                   | (20,000    | ) |                                                                 |  
|Increase (decrease) in accounts payable                                                                            |  |                   | (4,000     | ) |                                                                 |  
|Increase (decrease) in accrued expenses                                                                            |  |                   | 66,000     |   |                                                                 |  
|                                                                                                                   |  |                   |            |   |                                                                 |  
|Net cash provided (used) by operating activities                                                                   |  |                   | (596,000   | ) |                                                                 |  
|                                                                                                                   |  |                   |            |   |                                                                 |  
|Cash flows from investing activities:                                                                              |  |                   |            |   |                                                                 |  
|Purchase of available-for-sale marketable securities                                                               |  |                   | (9,892,000 | ) |                                                                 |  
|Proceeds from sale/maturity of available-for-sale marketable securities                                            |  |                   | 11,785,000 |   |                                                                 |  
|Proceeds from maturity of held-to-maturity marketable securities                                                   |  |                   |           |   |                                                                 |  
|Proceeds from sale of equipment                                                                                    |  |                   |           |   |                                                                 |  
|Purchase of fixed assets                                                                                           |  |                   |           |   |                                                                 |  
|Investment in Oragen                                                                                               |  |                   |           |   |                                                                 |  
|Investment in Colloral LLC                                                                                         |  |                   |           |   |                                                                 |  
|Increase in patent costs                                                                                           |  |                   |           |   |                                                                 |  
|Increase in other assets                                                                                           |  |                   |           |   |                                                                 |  
|                                                                                                                   |  |                   |            |   |                                                                 |  
|Net cash provided (used) by investing activities                                                                   |  |                   | 1,893,000  |   |                                                                 |  
|                                                                                                                   |  |                   |            |   |                                                                 |  
|Cash flows from financing activities:                                                                              |  |                   |            |   |                                                                 |  
|Proceeds from sale-leaseback of fixed assets                                                                       |  |                   |           |   |                                                                 |  
|Payments on obligations under capital leases                                                                       |  |                   |           |   |                                                                 |  
|Net proceeds from issuance of mandatorily redeemable convertible preferred stock                                   |  |                   |           |   |                                                                 |  
|Proceeds from bridge notes                                                                                         |  |                   |           |   |                                                                 |  
|Proceeds from issuance of common stock                                                                             |  |                   |           |   |                                                                 |  
|Proceeds from issuance of convertible notes payable                                                                |  |                   |           |   |                                                                 |  
|                                                                                                                   |  |                   |            |   |                                                                 |  
|Net cash provided by financing activities                                                                          |  |                   |           |   |                                                                 |  
|                                                                                                                   |  |                   |            |   |                                                                 |  
|Net increase in cash and cash equivalents                                                                          |  |                   | 1,297,000  |   |                                                                 |  
|Cash and cash equivalents, beginning of period                                                                     |  |                   | 3,929,000  |   |                                                                 |  
|                                                                                                                   |  |                   |            |   |                                                                 |  
|Cash and cash equivalents, end of period                                                                           |  | $                 | 5,226,000  |   |                                                                 | $
|                                                                                                                   |  |                   |            |   |                                                                 |  



The accompanying notes
are an integral part of these financial statements.



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AUTOIMMUNE INC.

(a development stage company)

NOTES TO THE UNAUDITED FINANCIAL STATEMENTS



|1. | Interim Financial Data
|-- | ----------------------



The interim financial data as of September 30, 2003, for the three and nine month periods ended September 30, 2002 and 2003 and for the period from
inception (September 9, 1988) through September 30, 2003 are unaudited, however, in the opinion of AutoImmune Inc. (AutoImmune or the Company), these interim data include all adjustments, consisting only of normal recurring
adjustments necessary for a fair statement of the results for these interim periods. These financial statements should be read in conjunction with the financial statements and the notes thereto for the year ended December 31, 2002 included in the
Companys Form 10-K. Results for interim periods are not necessarily indicative of results for the entire year.



|2. | Stock Compensation
|-- | ------------------



The Company accounts for stock-based compensation using the intrinsic based method prescribed in Accounting Principles Board Opinion (APB) No.
25, Accounting for Stock Issued to Employees. The Company applies the disclosure requirements of Statement of Financial Accounting Standards (SFAS) No. 123, Accounting for Stock-Based Compensation. Accordingly, no compensation cost has
been recognized for options granted to employees with exercise prices equal to or greater than the fair market value of the common stock at the grant date. Had compensation cost been determined based on the fair value at the time of grant consistent
with the provisions of SFAS No. 123, the Companys net income (loss) and net income (loss) per share would have been changed to the pro forma amounts indicated below:



|                                                                                                                    |  | Three months endedSeptember 30, |          |   | Nine months endedSeptember 30, |  
|------------------------------------------------------------------------------------------------------------------- |  | ------------------------------- | -------- | - | ------------------------------ | -
|                                                                                                                    |  | 2002                            |          |   | 2003                           |  
|Net income (loss):                                                                                                  |  |                                 |          |   |                                |  
|As reported                                                                                                         |  | $                               | (245,000 | ) |                                | $
|Deduct: total stock-based employee compensation expense determined under the fair-value-based method for all
awards |  |                                 | (31,000  | ) |                                |  
|                                                                                                                    |  |                                 |          |   |                                |  
|Pro forma                                                                                                           |  | $                               | (276,000 | ) |                                | $
|                                                                                                                    |  |                                 |          |   |                                |  
|Net income (loss) per share - basic:                                                                                |  |                                 |          |   |                                |  
|As reported                                                                                                         |  | $                               | (0.01    | ) |                                | $
|Pro forma                                                                                                           |  |                                 | (0.02    | ) |                                |  
|Net income (loss) per share - diluted:                                                                              |  |                                 |          |   |                                |  
|As reported                                                                                                         |  | $                               | (0.01    | ) |                                | $
|Pro forma                                                                                                           |  |                                 | (0.02    | ) |                                |  



The fair value of each
option grant is estimated on the date of grant using the Black-Scholes option pricing model with the following weighted average assumptions used for grants in 2002 and 2003: no dividend yield for all years; expected volatility of 70% for 2002 and
75% for 2003, risk free interest rates ranging from 1.62% to 4.49% and a weighted average expected option term ranging from 2.6 to 6 years. Because additional option grants are expected to be made in the future, the pro forma impact on the three and
nine month periods ended September 30, 2003 is not representative of the pro forma effects which may be expected in future periods.



|3. | Net Loss Per Share - Basic and Diluted
|-- | --------------------------------------



Basic earnings (loss) per share is calculated based on the weighted average number of common shares outstanding during the period. Diluted earnings per
share is calculated based on the weighted average number of common shares and dilutive common equivalent shares assumed outstanding during the period. Shares used to compute diluted earnings per share for the three month periods ended September 30,
2002 and 2003 excluded 168,559 and 403,917 common share equivalents, respectively, as their inclusion would have been anti-dilutive. Shares used to compute diluted earnings per share for the nine month period ended September 30, 2002 excluded
101,546 common share equivalents, as their inclusion would have been anti-dilutive. For the nine month period ended September 30, 2003, the difference between weighted average shares outstanding basic and diluted is due to the effect of stock
options with exercise prices less than the average market value of the common stock. At September 30, 2003, stock options to purchase 576,483 weighted shares of common stock were outstanding with exercise prices greater than the fair value of the
common stock and accordingly, were excluded from the calculation of diluted net income per share.



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AUTOIMMUNE INC.

(a development stage company)



NOTES TO THE UNAUDITED FINANCIAL STATEMENTS



|4. | Cash Equivalents and Marketable Securities
|-- | ------------------------------------------



The following is a summary of cash equivalents held by the Company. Cash equivalents are carried at fair market value, which approximated amortized cost
at December 31, 2002 and September 30, 2003:



|             |  | December 31,2002 |           | September 30,2003
|------------ |  | ---------------- | --------- | -----------------
|Money market |  | $                | 5,024,000 |                  
|             |  |                  |           |                  
|             |  | $                | 5,024,000 |                  
|             |  |                  |           |                  



The
following is a summary of available-for-sale marketable securities held by the Company at December 31, 2002 and September 30, 2003:



|                                |  | Maturity Term         |  | Fair value |           | Unrealized gains |   | Unrealized losses |  | Amortizedcost
|------------------------------- |  | --------------------- |  | ---------- | --------- | ---------------- | - | ----------------- |  | -------------
|December 31, 2002               |  |                       |  |            |           |                  |   |                   |  |              
|U.S. Government debt securities |  | within 1 year         |  | $          | 4,985,000 |                  | $ | 4,000             |  | $            
|                                |  |                       |  |            |           |                  |   |                   |  |              
|September 30, 2003              |  |                       |  |            |           |                  |   |                   |  |              
|U.S. Government debt securities |  | within 1 year         |  | $          | 2,969,000 |                  | $ | 2,000             |  | $            
|U.S. Government debt securities |  | Between 1 and 2 years |  | $          | 2,060,000 |                  | $ |                  |  | $            
|Corporate debt securities       |  | Within 1 year         |  | $          | 3,426,000 |                  | $ |                  |  | $            
|                                |  |                       |  |            |           |                  |   |                   |  |              
|                                |  |                       |  | $          | 8,455,000 |                  | $ | 2,000             |  | $            
|                                |  |                       |  |            |           |                  |   |                   |  |              



Gross realized gains
and losses on sales of marketable securities for the three and nine month periods ended September 30, 2002 and 2003 were not significant.



Marketable securities which were purchased and sold in periods prior to adoption of Statement of Financial Accounting Standards (SFAS) No. 115 on January
1, 1994, other than held-to-maturity marketable securities, are included in the category available-for-sale marketable securities in the period from inception column of the statement of cash flows.



|5. | Other Assets
|-- | ------------



Colloral LLC is a joint venture created in August 2002 between AutoImmune and Deseret Laboratories Inc., (a private company headquartered in St. George,
Utah) to manufacture, market and sell Colloral®, a
product for nutritional support of patients with rheumatoid arthritis. AutoImmunes interest in Colloral LLC is greater than 50% but AutoImmune does not have control of Colloral LLC. Therefore, the investment is accounted for using the equity
method. In 2002 AutoImmune contributed the equipment used to manufacture bulk product and a license to certain Colloral-related intellectual property to Colloral LLC. These assets had a net book value of $0. Deseret contributed cash and is committed
to providing additional amounts, which additional amounts are refundable if the Board determines that they are no longer needed. In September 2003, AutoImmune and Deseret each contributed $25,000 to support a sales and marketing initiative.
AutoImmune is not obligated to make additional capital commitments, but may do so in the future.



The investment was initially recorded by AutoImmune at the carrying value of the contributed assets which was $0 and was increased to reflect the cash
contribution paid in September 2003. Profits and losses will be allocated in accordance with the joint venture agreement. The Companys equity in prior accumulated net losses is greater than $25,000,



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AUTOIMMUNE INC.

(a development stage company)



NOTES TO THE UNAUDITED FINANCIAL STATEMENTS



therefore, the additional investment has been reduced by the full $25,000. Under equity accounting, AutoImmune will not recognize a gain on this investment until AutoImmunes share of the profits of Colloral LLC exceeds its share of
the cumulative losses. As of September 30, 2003, Colloral has not generated any profit; therefore, the investment is carried at $0.



|6. | License Revenue and Warrant
|-- | ---------------------------



In March 2003, the Company received a $1,500,000 payment from a subsidiary of Elan Plc (Elan) for the purchase of certain patent rights
related to Alzheimers disease. The payment from Elan was the third and final payment pursuant to an agreement between Elan and the Company dated effective January 29, 2000. In conjunction with receiving the payment, the Company issued a
warrant to Elan to purchase 375,000 shares of the Companys common stock at $0.73 per share. The warrant expires five years from the date of issuance. Therefore, the valuation of these warrants, as determined by the Black-Scholes method, of
$155,000 was recorded as an offset to revenue during the first quarter of 2003. In addition, the Company paid The Brigham and Womens Hospital (BWH) $75,000. This amount represents a portion of the cash payment received from the
Elan as required under the current research and development agreement with BWH.



|7. | Accumulated Other Comprehensive Income
|-- | --------------------------------------



In the first quarter of 1998, the Company adopted SFAS No. 130, Reporting Comprehensive Income. This statement requires disclosure of comprehensive
income and its components in interim and annual reports. The components of comprehensive income (loss) consisted of the following:



|                                      |  | For the three months endedSeptember 30, |          |   | For the nine months endedSeptember 30, |  
|------------------------------------- |  | --------------------------------------- | -------- | - | -------------------------------------- | -
|                                      |  | 2002                                    |          |   | 2003                                   |  
|Net income (loss)                     |  | $                                       | (245,000 | ) |                                        | $
|Unrealized gain (loss) on investments |  |                                         |         |   |                                        |  
|                                      |  |                                         |          |   |                                        |  
|Comprehensive income (loss)           |  | $                                       | (245,000 | ) |                                        | $
|                                      |  |                                         |          |   |                                        |  



|8. | Indemnification
|-- | ---------------



The Company enters into standard indemnification agreements in its ordinary course of business. Pursuant to these agreements, the Company indemnifies,
holds harmless, and agrees to reimburse the indemnified party for losses suffered or incurred by the indemnified party, generally its business partners, in connection with any U.S. patent, or any copyright or other intellectual property infringement
claim by any third party with respect to its products. The term of these indemnification agreements is generally perpetual any time after execution of the agreement. The maximum potential amount of future payments that could be required under these
indemnification agreements is unlimited. The Company has never incurred costs to defend lawsuits or settle claims related to these indemnification agreements. As a result, the estimated fair value of these agreements is minimal.



|9. | Recent Accounting Pronouncements
|-- | --------------------------------



In January 2003, the Financial Accounting Standards Board (FASB) issued FASB Interpretation No. 46 (FIN 46), Consolidation
of Variable Interest Entities, and Interpretation of Accounting Research Bulletin No. 51. FIN 46 requires certain variable interest entities (VIE), to be consolidated by the primary beneficiary of the entity if the equity investors
in the entity do not have the characteristics of a controlling financial interest or do not have sufficient equity at risk for the entity to finance its activities without additional subordinated financial support from other parties. FIN 46 is
effective for all VIE created or acquired after January 31, 2003. For VIE created or acquired prior to February 1, 2003, the provisions of FIN 46 must be applied for the first interim or annual period ending after December 15, 2003. The Company
believes Colloral LLC might be considered a VIE and has included transitional disclosures required by FIN 46. The Company is currently assessing the impact that the adoption of FIN 46 will have on its financial position and results of operation.



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AUTOIMMUNE INC.



ITEM 2.    MANAGEMENTS DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS



Results of Operations



Overview



This section,
Managements Discussion and Analysis of Financial Condition and Results of Operations contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, Section 27A of the Securities Act
of 1933 and Section 21E of the Securities Exchange Act of 1934 which involve risks and uncertainties. The Companys actual results may differ significantly from results discussed in the forward-looking statements due to a number of important
factors, including, but not limited to, the Companys extremely limited operations, the uncertainties of clinical trial results and product development, the Companys dependence on third parties for licensing and other revenue and risks of
technological change and competition. These factors are more fully discussed in the Companys most recent Annual Report on Form 10-K filed with the Securities and Exchange Commission in the section Business-Factors to be Considered.
The discussion in the Annual Report on Form 10-K is hereby incorporated by reference into this Quarterly Report.



Since its inception through September 30, 2003, the Company has incurred ongoing losses from operations and has cumulative losses as of September 30, 2003
totaling $107,623,000. To date, the Company has not recorded any revenue from the sale of products. Revenues recorded through September 30, 2003 were earned in connection with license rights, contract research and the granting of certain short-term
rights. As a result, inflation has not materially affected the Companys revenues and income from continuing operations.



In August 2002, the Company and Deseret Laboratories, Inc. entered into a joint venture by forming an entity called Colloral LLC to manufacture, market
and sell Colloral as a nutraceutical. The Companys interest in Colloral LLC is greater than 50%, but the Company does not have control of Colloral LLC. Therefore, the investment is accounted for using the equity method. To the extent that
Colloral LLC generates revenues in excess of cumulative losses, the Company will record income. In February 2003, Colloral LLC began marketing Colloral through direct mail solicitation of individuals who had previously expressed interest in
obtaining the product. It is anticipated that sales channels and promotional support will be expanded in the future, but there can be no assurance that the Company will derive income from this arrangement. Accordingly, the Company may continue to
incur substantial losses.



Three and Nine Month Periods Ended September 30,
2002 and 2003



Revenue was $18,000 and $25,000 for the
three month periods ended September 30, 2002 and 2003, respectively. Revenue was $48,000 and $1,415,000 for the nine month periods ended September 30, 2002 and 2003, respectively. In the first quarter of 2003, revenue was comprised of a $1,500,000
payment by a subsidiary of Elan Plc (Elan) for the purchase of certain patent rights related to Alzheimers disease net of warrants valued at $155,000 granted to Elan and monthly license payments from BioMS Medical Corporation
(BioMS). The revenue in 2002 and the remainder of 2003 was comprised of monthly license payments from BioMS. The payment from Elan was the third and final payment pursuant to the agreement entered into between Elan and the Company dated
effective January 29, 2000. Under the terms of this agreement, AutoImmune and BWH have indemnified Elan against any claim, demand or action arising from any misrepresentation made to Elan about patent rights and warranties.



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Research and development expenses were $211,000 and $70,000 for the three month periods ended September 30, 2002 and 2003,
respectively. The decrease is due to the timing of patent related legal costs. Research and development expenses were $329,000 and $241,000 for the nine month periods ended September 30, 2002 and 2003, respectively. The decrease is due to the timing
of patent related legal costs and offset by the amount of contractual payments to The Brigham and Womens Hospital under a research and development agreement, including $75,000 of the payment received from Elan in the first quarter of 2003.



General and administrative expenses were $100,000 and $114,000
for the three month periods ended September 30, 2002 and 2003, respectively. General and administrative expenses were $506,000 and $508,000 for the nine month periods ended September 30, 2002 and 2003, respectively. The increase is due to higher
insurance costs offset by a decrease in professional service expenses.



Interest income was $48,000 and $29,000 for the three month periods ended September 30, 2002 and 2003, respectively. Interest income was $149,000 and $95,000 for the nine month periods ended September 30, 2002 and 2003, respectively. The
decrease is due to a lower average return on investment.



Liquidity and
Capital Resources



The Companys needs for funds have
historically fluctuated from period to period as it has increased or decreased the scope of its research and development activities. Since inception, the Company has funded these needs almost entirely through sales of its equity securities. Its
current needs have been significantly reduced as a result of the termination of AutoImmunes direct research, development activities, all full-time employees and certain other operating expenses in 1999.



As of October 2003, the Company had renewed its contractual obligation to The
Brigham and Womens Hospital to sponsor research. In addition, the Company holds an interest in an entity called Colloral LLC, which is manufacturing, marketing and selling Colloral as a nutraceutical. In September 2003, the Company and Deseret
each contributed $25,000 to support a sales and marketing initiative. The Company has no obligation to make additional capital contributions to Colloral LLC, but may do so in the future. To the extent that Colloral LLC generates income in excess of
cumulative losses, the Company may receive a cash distribution.



The Companys working capital and capital requirements will depend on numerous factors, including the strategic direction that the Company and its shareholders choose, the level of resources that the Company devotes to the development
of its patented products, the extent to which it proceeds by means of collaborative relationships with pharmaceutical or nutraceutical companies and its competitive environment. Based upon its budget for the calendar years 2003 and current
expectations for future years, the Company believes that current cash and marketable securities, and the interest earned from the investment thereof, will be sufficient to meet the Companys operating expenses and capital requirements for at
least five years. At the appropriate time, the Company may seek additional funding through public or private equity or debt financing, collaborative arrangements with pharmaceutical companies or from other sources. If additional funds are necessary
but not available, the Company will have to reduce or not pursue certain activities, which could include areas of research, product development, marketing activity, or otherwise modify its business strategy. Such a reduction would have a material
adverse effect on the Company.



In order to preserve principal
and maintain liquidity, the Companys funds are currently invested in U.S. Treasury obligations, high-grade corporate obligations and money market instruments. As of September 30, 2003, the Companys cash and cash equivalents and
marketable securities totaled $10,864,000. Current liabilities at September 30, 2003 were $118,000.



Off-Balance Sheet Arrangements



AutoImmune has not created, and is not party to, any special-purpose or off-balance sheet entities for the purpose of raising capital, incurring debt or operating parts of its business that are not consolidated into its financial statements
other than Colloral LLC.



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Critical Accounting Policies and Estimates



The preparation of financial statements in conformity with generally accepted accounting principles requires management to make estimates and judgments
that affect the reported amount of assets, liabilities, revenues and expenses, and related disclosure of contingent assets and liabilities. Management bases its estimates on historical experience and on various other assumptions that are believed to
be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates
under different assumptions or conditions.



The Company
believes the following critical accounting policies affect its more significant judgments and estimates used in the preparation of its financial statements:



Revenue is recognized in accordance with the Securities and Exchange Commissions Staff Accounting Bulletin (SAB) No. 101, Revenue
Recognition in Financial Statements. Revenue is recognized when the following criteria have been met: persuasive evidence of an arrangement exists; delivery has occurred and risk of loss has passed; the sellers price to the buyer is fixed
or determinable, and collectibility is reasonably assured.



Contract and license fee revenue is primarily generated through collaborative license and development agreements with strategic partners for the development and commercialization of the Companys product candidates. The terms of the
agreements typically include non-refundable license fees, funding of research and development, payments based upon achievement of certain milestones, or royalties on net product sales. Revenue arrangements where multiple products or services are
sold together under one contract are evaluated to determine if each element represents a separate earnings process. In the event that an element of such multiple element arrangement does not represent a separate earnings process, revenue from this
element is recognized over the term of the related contract.



Where the Company has continuing performance obligations under the terms of a collaborative arrangement or associated with non-refundable license fees, revenue is recognized over the period the Company completes its performance obligations.
Under the terms of one agreement, the Company and The Brigham and Womens Hospital have indemnified a subsidiary of Elan against any claim, demand or action arising from any misrepresentation made to the subsidiary of Elan about patent rights
and warranties, up to the amounts previously received by the Company under the agreement. The Company does not consider this a performance obligation that would preclude or defer revenue recognition. Option fees representing payments to be made to
the Company for a right to evaluate and negotiate the terms of a potential licensing arrangement are recognized when the options are granted because such fees are non-refundable and the Company has no further obligations.



Revenues from milestone payments related to arrangements under which the
Company has no continuing performance obligations are recognized upon achievement of the related milestone. Revenues from milestone payments related to arrangements under which the Company has continuing performance obligations are recognized as
revenue upon achievement of the milestone only if all of the following conditions are met: the milestone payments are non-refundable; substantive effort is involved in achieving the milestone; and the amount of the milestone is reasonable in
relation to the effort expended or the risk associated with achievement of the milestone. If any of these conditions are not met, the milestone payments are deferred and recognized as revenue over the term of the arrangement as the Company completes
its performance obligations.



Revenue from service contracts is
earned as the related services are performed.



Marketable
securities are considered to be impaired when a decline in fair value below cost basis is determined to be other than temporary. The company employs a methodology in evaluating whether a decline in fair value below costs basis is other than
temporary that considers available evidence regarding its marketable securities. In the event that the cost basis of a security exceeds its fair value, the Company



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evaluates, among other factors: the duration of the period that, and extent to which, the fair value is less than the cost basis; the
financial health of and business outlook for the issuer of the securities, including industry and sector performance, changes in technology and operational and financing cash flow factors; overall market conditions and trends; and the Companys
intent and ability to hold the investment. Once a decline in fair value is determined to be other than temporary, a write-down is recorded and a new cost basis in the security is established. Assessing the above factors involves inherent
uncertainty. Accordingly, write-downs, if recorded, could be materially different from the actual market performance of marketable securities in the Companys portfolio, if, among other things, relevant information related to its marketable
securities was not publicly available or other factors not considered would have been relevant to the determination of impairment.



Recent Accounting Pronouncements



In January 2003, the Financial Accounting Standards Board (FASB) issued FASB Interpretation No. 46 (FIN 46), Consolidation
of Variable Interest Entities, and Interpretation of Accounting Research Bulletin No. 51. FIN 46 requires certain variable interest entities (VIE), to be consolidated by the primary beneficiary of the entity if the equity investors
in the entity do not have the characteristics of a controlling financial interest or do not have sufficient equity at risk for the entity to finance its activities without additional subordinated financial support from other parties. FIN 46 is
effective for all VIE created or acquired after January 31, 2003. For VIE created or acquired prior to February 1, 2003, the provisions of FIN 46 must be applied for the first interim or annual period ending after December 15, 2003. The Company
believes Colloral LLC would be considered a VIE and has included transitional disclosures required by FIN 46. The Company is currently assessing the impact that the adoption of FIN 46 will have on its financial position and results of operation.



ITEM 3.    QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK



The Company has invested all of its cash in U.S. Treasury obligations, high-grade corporate obligations and money market instruments. These investments
are denominated in U.S. dollars. Due to the conservative nature of these instruments, the Company does not believe that it has material exposure to interest rate or market risk.



ITEM 4.    CONTROLS AND PROCEDURES



(a)    Evaluation of Disclosure Controls and Procedures



The Companys Chief Executive Officer and Director of Finance and Treasurer evaluated the effectiveness of the Companys disclosure controls and
procedures (as defined in Rule 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934) as of September 30, 2003. Based upon this evaluation, the Companys Chief Executive Officer and Director of Finance and Treasurer conclude that,
as of September 30, 2003, the Companys disclosure controls and procedures were effective in providing reasonable assurance that the information required to be disclosed by the Company in the reports that it files or submits under the Exchange
Act has been recorded, processed, summarized and reported within the time periods specified in the SECs rules and forms.



There have been no changes in the companys internal control over financial reporting (as defined in Rule 13a-15(f) and  15d-15(f) under the
Securities Exchange Act of 1934) during the three months ended September 30, 2003 that have materially affected or are reasonably likely to materially affect the Companys internal control over financial reporting.



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PART IIOTHER INFORMATION



ITEM 6.     EXHIBITS AND REPORTS ON FORM 8-K



Item 6(a)  Exhibits (numbered in accordance with Item 601 of Regulation S-K)





|Exhibit Number |  | Description                                                                                                                                                                                                     
|-------------- |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|               | 
|10.1           |  | Amendment to the Research and Development Agreement between The Brigham and Womens Hospital, Inc. and AutoImmune Inc.                                                                                          
|               | 
|31.1           |  | Certification of the Chief Executive Officer required by Rule 13a-15(e) or Rule 15d-15(e) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the
Sarbanes-Oxley Act of 2002          
|               | 
|31.2           |  | Certification of the Director of Finance and Treasurer required by Rule 13a-15(e) or Rule 15d-15(e) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of
the Sarbanes-Oxley Act of 2002
|               | 
|32.1           |  | Certification of the Chief Executive Officer furnished pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of Sarbanes-Oxley Act of 2002                                                     
|               | 
|32.2           |  | Certification of the Director of Finance and Treasurer furnished pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of Sarbanes-Oxley Act of
2002                                           



Item 6(b)  Reports on Form 8-K



A Form 8-K was filed on August 11, 2003 to furnish the Companys issuance of a press release on August 7, 2003 announcing its financial results for the quarter ended June 30, 2003. No other Form 8-K has been filed during the quarter
for which this report is filed.



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SIGNATURES



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





|                        |  |  |  | AUTOIMMUNE INC.            
|----------------------- |  |  |  | ---------------------------
|                        |  | 
|Date: November 13, 2003 |  |  |  | /s/    ROBERT C. BISHOP    
|                        |  |  | 
|                        |  |  |  |                            
|                        |  |  |  |                            
|                        |  | 
|                        |  |  |  | /s/    HEATHER A. ELLERKAMP
|                        |  |  | 
|                        |  |  |  |                            





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