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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549





FORM 10-Q







|x | Quarterly report pursuant to Section 13 or 15 (d) of the Securities Exchange Act of 1934
|- | ----------------------------------------------------------------------------------------

For the Quarterly Period Ended September 30, 2008



| ̈ | Transition report pursuant to Section 13 or 15 (d) of the Securities Exchange Act of 1934
|- | -----------------------------------------------------------------------------------------

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

(Issuer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
a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See definitions of large accelerated filer, accelerated filer, and smaller reporting company in
Rule 12b-2 of the Exchange Act.:

Large accelerated filer   ̈        Accelerated filer   ̈        Non-accelerated filer   ̈        Smaller reporting company  x

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act.):    Yes  x    No   ̈

Number of shares outstanding of the registrants Common Stock as of November 6, 2008:



|                             |  |                              
|---------------------------- |  | -----------------------------
|Common Stock, par value $.01 |  | 16,999,623 shares outstanding









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##### Table of Contents

AUTOIMMUNE INC.

QUARTER ENDED SEPTEMBER 30, 2008

TABLE OF CONTENTS



|                                                                                                                                                                                                      |  |           
|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ----------
|                                                                                                                                                                                                      |  | PageNumber
|PART IFINANCIAL INFORMATION                                                                                                                                                                          |  |           
|                                                                                                                                                                                                      | 
|Item 1Financial Statements (Unaudited)                                                                                                                                                               |  |           
|                                                                                                                                                                                                      | 
|Consolidated Balance Sheet as of December 31, 2007 and September 30, 2008 (unaudited)                                                                                                                 |  | 3         
|                                                                                                                                                                                                      | 
|Consolidated Statement of Operations for the three and nine months ended September 
30, 2007 and 2008 and for the period from September 9, 1988 (date of inception) to September 30, 2008 (unaudited) |  | 4         
|                                                                                                                                                                                                      | 
|Consolidated Statement of Cash Flows for the nine months ended September 
30, 2007 and 2008 and for the period from September 9, 1988 (date of inception) to September 30, 2008 (unaudited)           |  | 5         
|                                                                                                                                                                                                      | 
|Notes to the Unaudited Consolidated Financial Statements                                                                                                                                              |  | 6         
|                                                                                                                                                                                                      | 
|Item 2Managements Discussion and Analysis of Financial Condition and Results of
Operations                                                                                                          |  | 10        
|                                                                                                                                                                                                      | 
|Item 3Quantitative and Qualitative Disclosures about Market Risk                                                                                                                                     |  | 13        
|                                                                                                                                                                                                      | 
|Item 4Controls and Procedures                                                                                                                                                                        |  | 13        
|                                                                                                                                                                                                      | 
|PART IIOTHER INFORMATION                                                                                                                                                                             |  |           
|                                                                                                                                                                                                      | 
|Item 6Exhibits                                                                                                                                                                                       |  | 14        
|                                                                                                                                                                                                      | 
|Signatures                                                                                                                                                                                            |  | 15        



2



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##### Table of Contents

PART IFINANCIAL INFORMATION



|ITEM 1. | FINANCIAL STATEMENTS
|------- | --------------------

AUTOIMMUNE INC.

(A development stage company)

CONSOLIDATED BALANCE SHEET

(Unaudited)



|                                                                                                                                                                                              |  |                  |              |   |                   |   |              |  
|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ---------------- | ------------ | - | ----------------- | - | ------------ | -
|                                                                                                                                                                                              |  | December 31,2007 |              |   | September 30,2008 |  
|ASSETS                                                                                                                                                                                        |  |                  |              |   |                   |   |              |  
|Current assets:                                                                                                                                                                               |  |                  |              |   |                   |   |              |  
|Cash and cash equivalents                                                                                                                                                                     |  | $                | 7,994,000    |   |                   | $ | 8,591,000    |  
|Marketable securities                                                                                                                                                                         |  |                  | 810,000      |   |                   |   |             |  
|Accounts receivable                                                                                                                                                                           |  |                  | 12,000       |   |                   |   | 5,000        |  
|Prepaid expenses, inventories and other current assets                                                                                                                                        |  |                  | 155,000      |   |                   |   | 149,000      |  
|                                                                                                                                                                                              |  |                  |              |   |                   |   |              |  
|Total current assets                                                                                                                                                                          |  |                  | 8,971,000    |   |                   |   | 8,745,000    |  
|                                                                                                                                                                                              |  |                  |              |   |                   |   |              |  
|Total assets                                                                                                                                                                                  |  | $                | 8,971,000    |   |                   | $ | 8,745,000    |  
|                                                                                                                                                                                              |  |                  |              |   |                   |   |              |  
|                                                                                                                                                                                              |  |                 
|LIABILITIES AND STOCKHOLDERS EQUITY                                                                                                                                                          |  |                  |              |   |                   |   |              |  
|Current liabilities:                                                                                                                                                                          |  |                  |              |   |                   |   |              |  
|Accounts payable                                                                                                                                                                              |  | $                | 9,000        |   |                   | $ | 1,000        |  
|Accrued professional fees                                                                                                                                                                     |  |                  | 99,000       |   |                   |   | 110,000      |  
|Deferred revenue                                                                                                                                                                              |  |                  | 20,000       |   |                   |   | 18,000       |  
|                                                                                                                                                                                              |  |                  |              |   |                   |   |              |  
|Total current liabilities                                                                                                                                                                     |  |                  | 128,000      |   |                   |   | 129,000      |  
|                                                                                                                                                                                              |  |                  |              |   |                   |   |              |  
|Commitments and contingencies                                                                                                                                                                 |  |                  |              |   |                   |   |              |  
|Minority interest in joint venture                                                                                                                                                            |  |                  | 11,000       |   |                   |   | 24,000       |  
|Stockholders equity:                                                                                                                                                                         |  |                  |              |   |                   |   |              |  
|Preferred stock, $0.01 par value: 5,000,000 shares authorized; no shares issued and outstanding at December 31, 2007 and
September 30, 2008                                                   |  |                  |             |   |                   |   |             |  
|Common stock, $0.01 par value; 25,000,000 shares authorized; 16,979,623 shares issued and outstanding at December 31, 2007 and 16,999,623
shares issued and outstanding at September 30, 2008 |  |                  | 170,000      |   |                   |   | 170,000      |  
|Additional paid-in capital                                                                                                                                                                    |  |                  | 118,420,000  |   |                   |   | 118,399,000  |  
|Deficit accumulated during the development stage                                                                                                                                              |  |                  | (109,761,000 | ) |                   |   | (109,977,000 | )
|Accumulated other comprehensive income                                                                                                                                                        |  |                  | 3,000        |   |                   |   |             |  
|                                                                                                                                                                                              |  |                  |              |   |                   |   |              |  
|Total stockholders equity                                                                                                                                                                    |  |                  | 8,832,000    |   |                   |   | 8,592,000    |  
|                                                                                                                                                                                              |  |                  |              |   |                   |   |              |  
|Total liabilities stockholders equity                                                                                                                                                        |  | $                | 8,971,000    |   |                   | $ | 8,745,000    |  
|                                                                                                                                                                                              |  |                  |              |   |                   |   |              |  

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



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AUTOIMMUNE INC.

(A development stage company)

CONSOLIDATED STATEMENT OF OPERATIONS

(Unaudited)



|                                                                |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|--------------------------------------------------------------- |  | ------------------ | ---------- | - | ----------------- | - | ---------- | -------------------------------------------------------------------- |  | - | ----------------- | - |  | - | ---------- | - |  | - | ------------ | -
|                                                                |  | Three months ended |            |   | Nine months ended |   |            | Period fromSeptember 9, 1988(date of inception)to September 30, 2008 | 
|                                                                |  | September 30,2007  |            |   | September 30,2008 |   |            | September 30,2007                                                    |  |   | September 30,2008 |   | 
|Revenue:                                                        |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|License rights                                                  |  | $                  | 45,000     |   |                   | $ | 45,000     |                                                                      |  | $ | 135,000           |   |  | $ | 135,000    |   |  | $ | 7,658,000    |  
|Option fees                                                     |  |                    | 3,000      |   |                   |   | 1,000      |                                                                      |  |   | 8,000             |   |  |   | 3,000      |   |  |   | 2,213,000    |  
|Research and development revenue under collaborative agreements |  |                    |           |   |                   |   |           |                                                                      |  |   |                  |   |  |   |           |   |  |   | 955,000      |  
|Product revenue                                                 |  |                    | 11,000     |   |                   |   | 11,000     |                                                                      |  |   | 76,000            |   |  |   | 87,000     |   |  |   | 431,000      |  
|                                                                |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|Total revenue                                                   |  |                    | 59,000     |   |                   |   | 57,000     |                                                                      |  |   | 219,000           |   |  |   | 225,000    |   |  |   | 11,257,000   |  
|                                                                |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|Costs and expenses:                                             |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|Cost of product revenue                                         |  |                    | 9,000      |   |                   |   | 1,000      |                                                                      |  |   | 20,000            |   |  |   | 29,000     |   |  |   | 100,000      |  
|Research and development:                                       |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|Related party                                                   |  |                    | 3,000      |   |                   |   | 3,000      |                                                                      |  |   | 9,000             |   |  |   | 9,000      |   |  |   | 20,004,000   |  
|All other                                                       |  |                    | 4,000      |   |                   |   |           |                                                                      |  |   | 86,000            |   |  |   | 84,000     |   |  |   | 92,873,000   |  
|Selling, general and administrative                             |  |                    | 163,000    |   |                   |   | 125,000    |                                                                      |  |   | 532,000           |   |  |   | 511,000    |   |  |   | 21,965,000   |  
|                                                                |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|Total costs and expenses                                        |  |                    | 179,000    |   |                   |   | 129,000    |                                                                      |  |   | 647,000           |   |  |   | 633,000    |   |  |   | 134,942,000  |  
|                                                                |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|Total operating loss                                            |  |                    | (120,000   | ) |                   |   | (72,000    | )                                                                    |  |   | (428,000          | ) |  |   | (408,000   | ) |  |   | (123,685,000 | )
|                                                                |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|Interest income                                                 |  |                    | 112,000    |   |                   |   | 51,000     |                                                                      |  |   | 335,000           |   |  |   | 195,000    |   |  |   | 14,306,000   |  
|Interest expense                                                |  |                    |           |   |                   |   |           |                                                                      |  |   |                  |   |  |   |           |   |  |   | (303,000     | )
|Minority interest in joint venture                              |  |                    |           |   |                   |   | (2,000     | )                                                                    |  |   | 6,000             |   |  |   | (3,000     | ) |  |   | 9,000        |  
|Equity in net loss of unconsolidated affiliate                  |  |                    |           |   |                   |   |           |                                                                      |  |   |                  |   |  |   |           |   |  |   | (250,000     | )
|Other income (expense)                                          |  |                    |           |   |                   |   |           |                                                                      |  |   | 25,000            |   |  |   |           |   |  |   | (50,000      | )
|                                                                |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|Net loss                                                        |  | $                  | (8,000     | ) |                   | $ | (23,000    | )                                                                    |  | $ | (62,000           | ) |  | $ | (216,000   | ) |  | $ | (109,973,000 | )
|                                                                |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|Net loss per share-basic                                        |  | $                  | (0.00      | ) |                   | $ | (0.00      | )                                                                    |  | $ | (0.00             | ) |  | $ | (0.01      | ) |  |   |              |  
|                                                                |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|Net loss per share-diluted                                      |  | $                  | (0.00      | ) |                   | $ | (0.00      | )                                                                    |  | $ | (0.00             | ) |  | $ | (0.01      | ) |  |   |              |  
|                                                                |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|Weighted average common shares outstanding-basic                |  |                    | 16,979,623 |   |                   |   | 16,999,623 |                                                                      |  |   | 16,967,504        |   |  |   | 16,998,820 |   |  |   |              |  
|                                                                |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  
|Weighted average common shares outstanding-diluted              |  |                    | 16,979,623 |   |                   |   | 16,999,623 |                                                                      |  |   | 16,967,504        |   |  |   | 16,998,820 |   |  |   |              |  
|                                                                |  |                    |            |   |                   |   |            |                                                                      |  |   |                   |   |  |   |            |   |  |   |              |  

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



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AUTOIMMUNE INC.

(A development stage company)

CONSOLIDATED STATEMENT OF CASH FLOWS

(Unaudited)



|                                                                                                                    |  |                   |            |   |                                                                      |   |           |   |  |   |              |  
|------------------------------------------------------------------------------------------------------------------- |  | ----------------- | ---------- | - | -------------------------------------------------------------------- | - | --------- | - |  | - | ------------ | -
|                                                                                                                    |  | Nine months ended |            |   | Period fromSeptember 9, 1988(date of inception)to September 30, 2008 |  
|                                                                                                                    |  | September 30,2007 |            |   | September 30,2008                                                    |   |          
|Cash flows from operating activities:                                                                               |  |                   |            |   |                                                                      |   |           |   |  |   |              |  
|Net loss                                                                                                            |  | $                 | (62,000    | ) |                                                                      | $ | (216,000  | ) |  | $ | (109,973,000 | )
|Adjustment to reconcile net income (loss) to net cash used by operating activities:                                 |  |                   |            |   |                                                                      |   |           |   |  |   |              |  
|Interest expense related to demand notes converted into Series A mandatorily redeemable convertible preferred stock |  |                   |           |   |                                                                      |   |          |   |  |   | 48,000       |  
|Patent costs paid with junior convertible preferred and common stock                                                |  |                   |           |   |                                                                      |   |          |   |  |   | 3,000        |  
|Valuation of warrants issued in conjunction with license revenue                                                    |  |                   |           |   |                                                                      |   |          |   |  |   | 347,000      |  
|Noncash stock compensation                                                                                          |  |                   | 58,000     |   |                                                                      |   | 94,000    |   |  |   | 225,000      |  
|Noncash contributions to joint venture from minority interest                                                       |  |                   | 6,000      |   |                                                                      |   | 10,000    |   |  |   | 33,000       |  
|Minority interest in joint venture                                                                                  |  |                   | (6,000     | ) |                                                                      |   | 3,000     |   |  |   | (9,000       | )
|Depreciation and amortization                                                                                       |  |                   |           |   |                                                                      |   |          |   |  |   | 4,464,000    |  
|Loss on sale/disposal of fixed assets                                                                               |  |                   |           |   |                                                                      |   |          |   |  |   | 642,000      |  
|Decrease in patent costs                                                                                            |  |                   |           |   |                                                                      |   |          |   |  |   | 563,000      |  
|Impairment of investment in OraGen                                                                                  |  |                   |           |   |                                                                      |   |          |   |  |   | 100,000      |  
|Equity in net loss of unconsolidated affiliate                                                                      |  |                   |           |   |                                                                      |   |          |   |  |   | 250,000      |  
|(Increase) decrease in accounts receivable                                                                          |  |                   | 50,000     |   |                                                                      |   | 7,000     |   |  |   | (5,000       | )
|(Increase) decrease in prepaid expenses and other current assets                                                    |  |                   | (10,000    | ) |                                                                      |   | 6,000     |   |  |   | (149,000     | )
|Increase (decrease) in accounts payable                                                                             |  |                   | 24,000     |   |                                                                      |   | (8,000    | ) |  |   | 1,000        |  
|Increase (decrease) in accrued expenses                                                                             |  |                   | 4,000      |   |                                                                      |   | 11,000    |   |  |   | 90,000       |  
|Increase (decrease) in deferred revenue                                                                             |  |                   | (7,000     | ) |                                                                      |   | (2,000    | ) |  |   | 2,318,000    |  
|                                                                                                                    |  |                   |            |   |                                                                      |   |           |   |  |   |              |  
|Net cash provided/(used) by operating activities                                                                    |  |                   | 57,000     |   |                                                                      |   | (95,000   | ) |  |   | (103,352,000 | )
|                                                                                                                    |  |                   |            |   |                                                                      |   |           |   |  |   |              |  
|Cash flows from investing activities:                                                                               |  |                   |            |   |                                                                      |   |           |   |  |   |              |  
|Purchase of available-for-sale marketable securities                                                                |  |                   | (3,693,000 | ) |                                                                      |   |          |   |  |   | (322,315,000 | )
|Proceeds from sale/maturity of available-for-sale marketable securities                                             |  |                   | 1,135,000  |   |                                                                      |   | 807,000   |   |  |   | 311,304,000  |  
|Proceeds from maturity of held-to-maturity marketable securities                                                    |  |                   |           |   |                                                                      |   |          |   |  |   | 11,011,000   |  
|Proceeds from sale of equipment                                                                                     |  |                   |           |   |                                                                      |   |          |   |  |   | 306,000      |  
|Purchase of fixed assets                                                                                            |  |                   |           |   |                                                                      |   |          |   |  |   | (5,288,000   | )
|Investment in OraGen                                                                                                |  |                   |           |   |                                                                      |   |          |   |  |   | (100,000     | )
|Investment in Colloral LLC                                                                                          |  |                   |           |   |                                                                      |   |          |   |  |   | (230,000     | )
|Related party receivable from joint venture partner                                                                 |  |                   | (163,000   | ) |                                                                      |   |          |   |  |   |             |  
|Increase in patent costs                                                                                            |  |                   |           |   |                                                                      |   |          |   |  |   | (563,000     | )
|Increase in other assets                                                                                            |  |                   |           |   |                                                                      |   |          |   |  |   | (125,000     | )
|                                                                                                                    |  |                   |            |   |                                                                      |   |           |   |  |   |              |  
|Net cash provided /(used) by investing activities                                                                   |  |                   | (2,721,000 | ) |                                                                      |   | 807,000   |   |  |   | (6,000,000   | )
|                                                                                                                    |  |                   |            |   |                                                                      |   |           |   |  |   |              |  
|Cash flows from financing activities:                                                                               |  |                   |            |   |                                                                      |   |           |   |  |   |              |  
|Proceeds from sale-leaseback of fixed assets                                                                        |  |                   |           |   |                                                                      |   |          |   |  |   | 2,872,000    |  
|Payments on obligations under capital leases                                                                        |  |                   |           |   |                                                                      |   |          |   |  |   | (2,872,000   | )
|Net proceeds from issuance of mandatorily redeemable convertible preferred stock                                    |  |                   |           |   |                                                                      |   |          |   |  |   | 10,011,000   |  
|Proceeds from bridge notes                                                                                          |  |                   |           |   |                                                                      |   |          |   |  |   | 300,000      |  
|Proceeds from issuance of common stock                                                                              |  |                   | 33,000     |   |                                                                      |   | 10,000    |   |  |   | 105,557,000  |  
|Proceeds from issuance of convertible notes payable                                                                 |  |                   |           |   |                                                                      |   |          |   |  |   | 2,200,000    |  
|Payments for repurchase of outstanding warrants                                                                     |  |                   |           |   |                                                                      |   | (125,000  | ) |  |   | (125,000     | )
|                                                                                                                    |  |                   |            |   |                                                                      |   |           |   |  |   |              |  
|Net cash provided/(used) by financing activities                                                                    |  |                   | 33,000     |   |                                                                      |   | (115,000  | ) |  |   | 117,943,000  |  
|                                                                                                                    |  |                   |            |   |                                                                      |   |           |   |  |   |              |  
|Net increase (decrease) in cash and cash equivalents                                                                |  |                   | (2,631,000 | ) |                                                                      |   | 597,000   |   |  |   | 8,591,000    |  
|Cash and cash equivalents, beginning of period                                                                      |  |                   | 8,763,000  |   |                                                                      |   | 7,994,000 |   |  |   |             |  
|                                                                                                                    |  |                   |            |   |                                                                      |   |           |   |  |   |              |  
|Cash and cash equivalents, end of period                                                                            |  | $                 | 6,132,000  |   |                                                                      | $ | 8,591,000 |   |  | $ | 8,591,000    |  
|                                                                                                                    |  |                   |            |   |                                                                      |   |           |   |  |   |              |  

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



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AUTOIMMUNE INC.

(a development stage company)

NOTES TO THE UNAUDITED CONSOLIDATED FINANCIAL
STATEMENTS



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

The interim financial data
as of September 30, 2008, for the three and nine months ended September 30, 2007 and 2008 and for the period from inception (September 9, 1988) through September 30, 2008 are unaudited; however, in our opinion the interim data
includes all adjustments, consisting only of normal recurring adjustments, necessary for a fair statement of the results for these interim periods. The consolidated balance sheet presented as of December 31, 2007 has been derived from our
audited consolidated financial statements as of that date. These financial statements should be read in conjunction with the financial statements and the notes thereto for the year ended December 31, 2007 included in our Form 10-KSB. Results
for interim periods are not necessarily indicative of results for the entire year. Certain amounts have been reclassified to conform to the current presentations. Our consolidated financial statements include the accounts of AutoImmune, Inc. and our
joint venture with Deseret Laboratories, Inc. (Deseret), Colloral LLC. Pursuant to Financial Accounting Standards Board (FASB) Interpretation No. 46, Consolidation of Variable Interest Entities (FIN
46), as revised by FIN 46R, we began to consolidate Colloral LLC in the third quarter of 2005 when it qualified as a variable interest entity of which we are the primary beneficiary. All significant intercompany accounts and transactions have
been eliminated in consolidation. Refer to note 6 for additional information related to our interest in Colloral LLC.



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

We have several stock-based
employee compensation plans. On January 1, 2006, we adopted Statement of Financial Accounting Standards (SFAS) No. 123R Accounting for Stock-Based Compensation using the modified prospective method, which results in
the provisions of SFAS No. 123R only being applied to the consolidated financial statements on a going-forward basis (that is, the prior period results have not been restated). Under the fair value recognition provisions of SFAS No.123R,
stock-based compensation cost is measured at the grant date based on the value of the award and is recognized as expense over the requisite service period. Stock-based employee compensation expense was $33,000 and $27,000 for the three months ended
September 30, 2007 and 2008, respectively, and $58,000 and $94,000 for the nine months ended September 30, 2007 and 2008, respectively, and are recorded as selling, general and administrative expense in the accompanying consolidated
statement of operations.



|3. | Net Income (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 outstanding during the period. For the three and nine month periods ended September 30, 2007 shares used to compute diluted earnings per share excluded 1,596,000 stock options and warrants as their inclusion would have
been anti-dilutive due to net losses incurred in these periods. For the three and nine month periods ended September 30, 2008, shares used to compute diluted earnings per share excluded 1,211,500 stock options as their inclusion would have been
anti-dilutive due to net losses incurred in these periods.



|4. | Fair Value Measurements
|-- | -----------------------

Effective January 1,
2008, we implemented Statement of Financial Accounting Standard No. 157, Fair Value Measurement, or SFAS 157, for our financial assets and liabilities that are re-measured and reported at fair value at each reporting period,
and non-financial assets and liabilities that are re-measured and reported at fair value at least annually. In accordance with the provisions of FSP No. FAS 157-2, Effective Date of FASB Statement No. 157, we have elected
to defer implementation of SFAS 157 as it relates to our non-financial assets and non-financial liabilities that are recognized and disclosed at fair value in the financial statements on a nonrecurring basis until January 1, 2009. We are
evaluating the impact, if any, this Standard will have on our non-financial assets and liabilities.

The adoption of SFAS 157 to our
financial assets and liabilities and non-financial assets and liabilities that are re-measured and reported at fair value at least annually did not have an impact on our financial results.



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The following table presents information about our assets that are measured at fair value on a recurring
basis as of September 30, 2008, and indicates the fair value hierarchy of the valuation techniques we utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize quoted prices (unadjusted) in active
markets for identical assets. Fair values determined by Level 2 inputs utilize data points that are observable such as quoted prices, interest rates and yield curves. Fair values determined by Level 3 inputs are unobservable data points
for the asset or liability, and included situations where there is little, if any, market activity for the asset:



|                 |  |                   |           |                                        |   |                                           |  |                                        |   |  |   |  
|---------------- |  | ----------------- | --------- | -------------------------------------- | - | ----------------------------------------- |  | -------------------------------------- | - |  | - | -
|                 |  | September 30,2008 |           | Quoted Pricesin ActiveMarkets(Level 1) |   | SignificantOtherObservableInputs(Level 2) |  | SignificantUnobservableInputs(Level
3)
|Assets:          |  |                   |           |                                        |   |                                           |  |                                        |   |  |   |  
|Cash equivalents |  | $                 | 8,591,000 |                                        | $ | 8,591,000                                 |  | $                                      |  |  | $ | 
|                 |  |                   |           |                                        |   |                                           |  |                                        |   |  |   |  
|Total            |  | $                 | 8,591,000 |                                        | $ | 8,591,000                                 |  | $                                      |  |  | $ | 
|                 |  |                   |           |                                        |   |                                           |  |                                        |   |  |   |  

The fair values of cash equivalents are determined through market, observable and corroborated
sources.

The carrying amounts reflected in the consolidated balance sheets for cash, accounts receivable, other current assets, accounts
payable and accrued expenses and other approximate fair value due to their short-term maturities.



|5. | Cash Equivalents and Marketable Securities
|-- | ------------------------------------------

Cash
equivalents are carried at amortized cost, which approximated fair value at December 31, 2007 and September 30, 2008, and were primarily invested in money market accounts and U.S. Government Agency debt securities.

The following is a summary of available-for-sale marketable securities held by us at December 31, 2007 which are carried at fair market value. We did
not hold any available-for-sale marketable securities at September 30, 2008.



|                                       |  |               |  |           |         |                 |   |                  |  |               |   |  |   |        
|-------------------------------------- |  | ------------- |  | --------- | ------- | --------------- | - | ---------------- |  | ------------- | - |  | - | -------
|                                       |  | Maturityterm  |  | FairValue |         | Unrealizedgains |   | Unrealizedlosses |  | Amortizedcost
|December 31, 2007:                     |  |               |  |           |         |                 |   |                  |  |               |   |  |   |        
|U.S. Government Agency debt securities |  | Within 1 year |  | $         | 810,000 |                 | $ | 3,000            |  | $             |  |  | $ | 807,000
|                                       |  |               |  |           |         |                 |   |                  |  |               |   |  |   |        
|                                       |  |               |  | $         | 810,000 |                 | $ | 3,000            |  | $             |  |  | $ | 807,000

Gross realized gains and losses on sales of marketable securities for the three months ended
September 30, 2008 were insignificant.

Marketable securities that were purchased and sold in periods prior to adoption of SFAS
No. 115 Accounting for Certain Investments in Debt and Equity Securities, 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.



|6. | Other Assets
|-- | ------------

OraGen Corporation
(OraGen) was a private company in which our interest was less than 20%. In 2002, we determined that the entire value of our investment in OraGen should be reduced to zero to reflect OraGens continued difficulty in obtaining funding
for its operations. In February 2004, Enzo Biochem, Inc. acquired the assets of OraGen. The final distribution of $25,000 was received in March 2007 and recorded as other income.

In August 2002, we entered into our joint venture with Deseret by forming Colloral LLC to
manufacture, market and sell Colloral® as a dietary supplement. Our interest in Colloral LLC was greater than 50% and we actively participated in its management, but we did not have voting
control of Colloral LLC and our share of distributions and allocations of profits and losses did not exceed 50%. Therefore, the investment had historically been accounted for using the equity method. In August 2005, we amended the Colloral LLC
operating agreement to increase our share of distributions and allocations of profits and losses in return for our commitment to fund 100% of the costs associated with the implementation of a marketing program for The Collagen Solution. As a result
of the amendments to the operating agreement, we are required to consolidate Colloral LLC in accordance with FIN 46R, effective in the third quarter of 2005. Under FIN 46R, Colloral LLC is considered a variable interest entity, of which we are the
primary beneficiary. In accordance with FIN 46R, we re-evaluate the provisions of FIN 46R when triggering events arise and, to date, no events have transpired which would require deconsolidation. Certain events may arise in the future, including
additional modifications to the operating agreement, which may require us to re-evaluate the joint venture under FIN 46R. Such re-evaluation may result in a conclusion that the joint venture is no longer a variable interest entity requiring
consolidation.



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##### Table of Contents

In accordance with the amendment to the Colloral LLC operating agreement, we made additional capital
contributions of $1,020,000 to Colloral LLC from 2003 through 2006. We satisfied our funding commitment in 2006, but we made additional contributions of $12,000 during the year ended December 31, 2007 to support continuing marketing efforts. No
capital contributions were made during the nine months ended September 30, 2008. We may make additional contributions to Colloral LLC in the future.

There can be no assurance that the sales and marketing initiatives for Colloral LLC that have been or, in the future, may be funded by our capital contributions will be successful. Accordingly, in the future we may
again incur substantial losses. Our financial statements reflect transactions with Colloral LLC on a consolidated basis beginning in the third quarter of 2005.

At December 31, 2007 and September 30, 2008, the excess of Deserets capital contributions over their portion of the accumulated losses is recorded as a minority interest liability in our consolidated
balance sheet. To the extent Deserets share of accumulated losses exceeds its capital contributions in the future, we would be required to recognize 100% of Colloral LLCs losses and if future earnings materialized, we would recognize
100% of Colloral LLCs net income to the extent of the Deseret losses we previously recognized.

The following table contains selected
financial data for Colloral LLC. Shipping and handling costs have been classified as selling expenses. The balance sheet amounts as of December 31, 2007 and September 30, 2008 and Colloral LLCs operating results for the three and
nine months ended September 30, 2007 and 2008 have been consolidated into our financial statements:



|                                            |  |                                 |         |                                |      |   |        |  |   |        |   |  |   |       
|------------------------------------------- |  | ------------------------------- | ------- | ------------------------------ | ---- | - | ------ |  | - | ------ | - |  | - | ------
|                                            |  | Three months endedSeptember 30, |         | Nine months endedSeptember 30,
|                                            |  | 2007                            |         |                                | 2008 |   | 2007   |  |   | 2008  
|Statement of Operations Data:               |  |                                 |         |                                |      |   |        |  |   |        |   |  |   |       
|Revenue                                     |  | $                               | 14,000  |                                |      | $ | 11,000 |  | $ | 84,000 |   |  | $ | 89,000
|Cost of goods sold                          |  | $                               | 9,000   |                                |      | $ | 1,000  |  | $ | 20,000 |   |  | $ | 29,000
|Selling, general and administrative expense |  | $                               | 34,000  |                                |      | $ | 8,000  |  | $ | 68,000 |   |  | $ | 46,000
|Net income (loss)                           |  | $                               | (29,000 | )                              |      | $ | 2,000  |  | $ | (4,000 | ) |  | $ | 14,000



|                      |  |                  |         |                   |   |        
|--------------------- |  | ---------------- | ------- | ----------------- | - | -------
|                      |  | December 31,2007 |         | September 30,2008
|Balance Sheet Data:   |  |                  |         |                   |   |        
|Current assets        |  | $                | 171,000 |                   | $ | 192,000
|Long term assets      |  |                  |        |                   |   |       
|Current liabilities   |  |                  | 5,000   |                   |   | 3,000  
|Long term liabilities |  |                  |        |                   |   |       

In 2000, we completed a market analysis of Colloral as a dietary supplement and subsequently filed
a Notice of New Dietary Ingredient with the FDA that was accepted without comment. On February 18, 2005, we received a letter from the FDA stating that the FDA reconsidered the information contained in our Notice of New Dietary
Ingredient and concluded that Colloral is not a dietary supplement but appears to be a drug under the Federal Food, Drug, and Cosmetic Act, and thus subject to the regulatory requirements for drugs. On April 15, 2005, we submitted a response to
the FDAs letter and hope to have demonstrated that the product meets the statutory definition of a dietary supplement. We cannot predict whether or not the FDA will agree with our position and what the effect of the FDAs letter will be.
It is possible that Colloral LLC and its licensed distributors will be unable to market the product as a dietary supplement and that the products will be subject to the regulatory requirements for drugs. If the FDA makes a final determination that
requires us to comply with the regulatory requirements for drugs, Colloral, The Collagen Solution and Vital 3 will be withdrawn from the market, which would eliminate the possibility of future distributions to us from Colloral LLC.



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##### Table of Contents

|7. | Accumulated Other Comprehensive Loss
|-- | ------------------------------------

The
components of comprehensive loss consisted of the following:



|                                                |  |                                         |        |   |                                        |   |         |      |  |   |         |   |  |   |          |  
|----------------------------------------------- |  | --------------------------------------- | ------ | - | -------------------------------------- | - | ------- | ---- |  | - | ------- | - |  | - | -------- | -
|                                                |  | For the three months endedSeptember 30, |        |   | For the nine months endedSeptember 30, |  
|                                                |  | 2007                                    |        |   | 2008                                   |   |         | 2007 |  |   | 2008    |  
|Net loss                                        |  | $                                       | (8,000 | ) |                                        | $ | (23,000 | )    |  | $ | (62,000 | ) |  | $ | (216,000 | )
|Change in unrealized gain (loss) on investments |  |                                         | 2,000  |   |                                        |   | (1,000  | )    |  |   | 2,000   |   |  |   | (3,000   | )
|                                                |  |                                         |        |   |                                        |   |         |      |  |   |         |   |  |   |          |  
|Comprehensive loss                              |  | $                                       | (6,000 | ) |                                        | $ | (24,000 | )    |  | $ | (60,000 | ) |  | $ | (219,000 | )
|                                                |  |                                         |        |   |                                        |   |         |      |  |   |         |   |  |   |          |  



|8. | Warrant redemption
|-- | ------------------

In March 2000, we entered an
agreement under which a subsidiary of Elan Plc purchased all of our rights to certain patent applications involving the treatment of Alzheimers Disease. In connection with the agreement, Elan Plc received a warrant to purchase 375,000 shares
of our common stock at $3.13 per share in September 2001 and a warrant to purchase 375,000 shares of our common stock at $0.7275 per share in March 2003. The warrant to purchase 375,000 shares of our common stock at $3.13 per share expired effective
September 16, 2006. On February 27, 2008, we entered into a securities redemption agreement to repurchase the warrant to purchase 375,000 shares of our common stock at $0.7275 from Elan Plc for $125,000 which was recorded as a reduction of
additional paid in capital.



|9. | Indemnification
|-- | ---------------

We enter into standard
indemnification agreements in the ordinary course of business. Pursuant to these agreements, we indemnify, hold harmless and agree to reimburse the indemnified party for losses suffered or incurred by the indemnified party, generally our business
partners, in connection with any U.S. patent, copyright or other intellectual property infringement claim by any third party with respect to our products. The term of these indemnification agreements is generally perpetual. The maximum potential
amount of future payments that could be required under these indemnification agreements is unlimited. We have 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.



|10. | Recent Accounting Pronouncements
|--- | --------------------------------

In December 2007,
the FASB issued SFAS No. 141R, Business Combinations. SFAS No. 141R, among other aspects, requires the acquiring entity in a business combination to recognize all (and only) the assets acquired and liabilities assumed in the
transaction, establishes the acquisition-date fair value as the measurement objective for all assets acquired and liabilities assumed, and requires the acquirer to disclose certain information to enable users to understand the nature and financial
effect of the business combination. The statement requires that cash outflows such as transaction costs and post-acquisition restructuring be charged to expense instead of capitalized as a cost of the acquisition. Contingent purchase price will be
recorded at its initial fair value and then re-measured as time passes through adjustments to net income. SFAS No. 141R is effective for us in 2009. We are currently evaluating the impact of adoption.

In December 2007, the FASB issued SFAS No. 160, Noncontrolling Interests in Consolidated Financial Statements. SFAS No. 160 will
change the accounting for minority interests, which will be reclassified as noncontrolling interests and classified as a component of equity. SFAS No. 160 is effective for us in 2009. We are currently evaluating the impact of adoption.

In December 2007, the EITF of the FASB reached a consensus on Issue No. 07-1, Accounting for Collaborative Arrangements.
The EITF established the definition of a collaborative arrangement and determined that revenues and costs incurred with third parties in connection with collaborative arrangements would be presented gross or net based on the criteria in
EITF 99-19 and other accounting literature. Based on the nature of the arrangement, payments to or from collaborators would be evaluated and the arrangements terms, the nature of the entitys business, and whether those payments are within
the scope of other accounting literature would be presented. Companies are also required to disclose the nature and purpose of collaborative arrangements along with the accounting policies and the classification and amounts of significant financial-
statement amounts related to the arrangements. Activities in the arrangement conducted in a separate legal entity should be accounted for under other accounting literature; however required disclosure under EITF 07-1 applies to the entire
collaborative agreement. EITF 07-1 is effective for us January 1, 2009 and is to be applied retrospectively to all periods presented for all collaborative arrangements existing as of the effective date. We do not expect the adoption of
EITF 07-1 to have a material impact on our consolidated financial statements.



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##### Table of Contents

AUTOIMMUNE INC.



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

Results of Operations

Overview

From our inception through September 30, 2008, we have incurred ongoing losses from operations and have cumulative losses as of September 30, 2008 totaling $109,973,000. To date, our only revenue from the
sale of products has been earned through our joint venture, Colloral LLC. The majority of revenues recorded from inception through September 30, 2008 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 our revenues and income from continuing operations.

In August 2002, we entered into our joint venture with Deseret by forming Colloral LLC to manufacture, market and sell Colloral® as a dietary supplement. Our
interest in Colloral LLC was greater than 50% and we actively participated in its management, but we did not have voting control of Colloral LLC and our share of distributions and allocations of profits and losses did not exceed 50%. Therefore, the
investment had historically been accounted for using the equity method. In August 2005, we amended the Colloral LLC operating agreement to increase our share of distributions and allocations of profits and losses in return for our commitment to fund
100% of the costs associated with the implementation of a marketing program for The Collagen Solution. As a result of the amendments to the operating agreement, we are required to consolidate Colloral LLC in accordance with FIN 46R, effective in the
third quarter of 2005. Under FIN 46R, Colloral LLC is considered a variable interest entity, of which we are the primary beneficiary. In accordance with FIN 46R, we re-evaluate the provisions of FIN 46R when triggering events arise and, to date, no
events have transpired which would require deconsolidation. Certain events may arise in the future, including additional modifications to the operating agreement, which may require us to re-evaluate the joint venture under FIN 46R. Such
re-evaluation may result in a conclusion that the joint venture is no longer a variable interest entity requiring consolidation.

In accordance with the
amendment to the Colloral LLC operating agreement, we made additional capital contributions of $1,020,000 to Colloral LLC from 2003 through 2006. We satisfied our funding commitment in 2006, but we made additional contributions of $12,000 during the
year ended December 31, 2007 to support continuing marketing efforts. No capital contributions were made during the nine months ended September 30, 2008. We may make additional contributions to Colloral LLC in the future.

There can be no assurance that the sales and marketing initiatives that have been or, in the future, may be funded by our capital contributions will be successful.
Accordingly, in the future we may again incur substantial losses. Our financial statements reflect transactions with Colloral LLC on a consolidated basis beginning in the third quarter of 2005.

The following table contains selected financial data for Colloral LLC. Shipping and handling costs have been classified as selling expenses. The balance sheet amounts as
of December 31, 2007 and September 30, 2008 and Colloral LLCs operating results for the three and nine months ended September 30, 2007 and 2008 have been consolidated into our financial statements:



|                                            |  |                                 |         |                                |      |   |        |  |   |        |   |  |   |       
|------------------------------------------- |  | ------------------------------- | ------- | ------------------------------ | ---- | - | ------ |  | - | ------ | - |  | - | ------
|                                            |  | Three months endedSeptember 30, |         | Nine months endedSeptember 30,
|                                            |  | 2007                            |         |                                | 2008 |   | 2007   |  |   | 2008  
|Statement of Operations Data:               |  |                                 |         |                                |      |   |        |  |   |        |   |  |   |       
|Revenue                                     |  | $                               | 14,000  |                                |      | $ | 11,000 |  | $ | 84,000 |   |  | $ | 89,000
|Cost of goods sold                          |  | $                               | 9,000   |                                |      | $ | 1,000  |  | $ | 20,000 |   |  | $ | 29,000
|Selling, general and administrative expense |  | $                               | 34,000  |                                |      | $ | 8,000  |  | $ | 68,000 |   |  | $ | 46,000
|Net income (loss)                           |  | $                               | (29,000 | )                              |      | $ | 2,000  |  | $ | (4,000 | ) |  | $ | 14,000



|                      |  |                  |         |                   |   |        
|--------------------- |  | ---------------- | ------- | ----------------- | - | -------
|                      |  | December 31,2007 |         | September 30,2008
|Balance Sheet Data:   |  |                  |         |                   |   |        
|Current assets        |  | $                | 171,000 |                   | $ | 192,000
|Long term assets      |  |                  |        |                   |   |       
|Current liabilities   |  |                  | 5,000   |                   |   | 3,000  
|Long term liabilities |  |                  |        |                   |   |       



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##### Table of Contents

In 2000, we completed a market analysis of Colloral as a dietary supplement and subsequently filed a Notice of New
Dietary Ingredient with the FDA that was accepted without comment. On February 18, 2005, we received a letter from the FDA stating that the FDA reconsidered the information contained in our Notice of New Dietary Ingredient and concluded
that Colloral is not a dietary supplement but appears to be a drug under the Federal Food, Drug, and Cosmetic Act, and thus subject to the regulatory requirements for drugs. On April 15, 2005, we submitted a response to the FDAs letter
and hope to have demonstrated that the product meets the statutory definition of a dietary supplement. We cannot predict whether or not the FDA will agree with our position and what the effect of the FDAs letter will be. It is possible that
Colloral LLC and its licensed distributors will be unable to market the product as a dietary supplement and that the products will be subject to the regulatory requirements for drugs. If the FDA makes a final determination that requires us to comply
with the regulatory requirements for drugs, Colloral, The Collagen Solution and Vital 3 will be withdrawn from the market, which would eliminate the possibility of future distributions to us from Colloral LLC.

Three and Nine Months Ended September 30, 2007 and 2008

Revenue
was $59,000 and $57,000 for the three months ended September 30, 2007 and 2008, respectively. Revenue was $219,000 and $225,000 for the nine months ended September 30, 2007 and 2008, respectively. The revenue in the three and nine months
ended September 30, 2007 and 2008 was comprised of monthly license payments from BioMS for their use of our patents pertaining to an injectable therapy for the treatment of multiple sclerosis, and option fees and product revenues generated
through our joint venture, Colloral LLC, the results of which are consolidated with our financial results. In 2006 and 2007, Colloral LLC executed a series of agreements with Futurebiotics, LLC and related companies whereby Futurebiotics began
marketing Collorals dietary supplement under the brand name, Vital 3, through several different channels, including the GNC chain of retail stores and both print and e-catalogs. Domestic retail store sales ceased in September 2007 and
Futurebiotics is currently selling product through print and e-catalogs through its affiliate, Bronson Laboratories, while it works on both international and domestic selling opportunities. Option payments related to the execution of the
Futurebiotics agreement are reflected as option fee revenue and are being amortized over the life of the agreement. Product shipped under these agreements generated no revenue during the three months ended September 30, 2007 and 2008, but
generated revenue of $29,000 and $26,000 during the nine months ended September 30, 2007 and 2008, respectively. Colloral LLC also contracted with The Shopping Channel of Canada to market Vital 3 through televised segments and through their
website. Product shipped under this agreement generated revenue of $0 and $3,000 during the three months ended September 30, 2007 and 2008, respectively, and revenue of $0 and $28,000 during the nine months ended September 30, 2007 and
2008, respectively. The remaining product revenue is generated through direct sales of Colloral and the Collagen Solution to Colloral LLCs customers through its website.

Cost of goods sold was $9,000 and $1,000 for the three months ended September 30, 2007 and 2008, respectively. Cost of goods sold was $20,000 and $29,000 for the nine months ended September 30, 2007 and
2008, respectively. Fluctuations in cost of good sold are related to the mix of product revenues to consumers versus distributors.

Research and development
expenses were $7,000 and $3,000 for the three months ended September 30, 2007 and 2008, respectively. Research and development expenses were $95,000 and $93,000 for the nine months ended September 30, 2007 and 2008, respectively. Patent
related maintenance fees and legal fees have remained consistent in support of our portfolio of intellectual property.

Selling, general and administrative
expenses were $163,000 and $125,000 for the three months ended September 30, 2007 and 2008, respectively. The decrease is primarily a result of a decrease of $22,000 in advertising costs incurred by our consolidated joint venture, Colloral LLC.
Selling, general and administrative expenses were $532,000 and $511,000 for the nine months ended September 30, 2007 and 2008, respectively. The decrease is a result of the aforementioned decrease of $22,000 in advertising costs incurred by our
consolidated joint venture, Colloral LLC, a decline in our Directors and Officers insurance costs of $15,000 and our reduction of legal costs of $15,000. These decreases are partially offset by an increase in the stock compensation costs from
$58,000 during the nine months ended September 30, 2007 to $94,000 during the nine months ended September 30, 2008.

Interest income was $112,000
and $51,000 for the three months ended September 30, 2007 and 2008, respectively. Interest income was $335,000 and $195,000 for the nine months ended September 30, 2007 and 2008, respectively. The decrease is due to a decline in money
market and bond yields and a lower average balance of cash and marketable securities available for investment.

Other income was $25,000 for the
nine months ended September 30, 2007. In February 2004, Enzo Biochem, Inc. acquired the assets of OraGen. In March 2007, the trustee received the final distribution of the proceeds in the amount of $25,000, which we have recorded as other
income.

Liquidity and Capital Resources

Our needs for
funds have historically fluctuated from period to period as we have increased or decreased the scope of our research and development activities. Since inception, we have funded these needs almost entirely through sales of our equity securities. Our
current needs have been significantly reduced as a result of the termination of our direct research and development activities, all full-time employees and other sources of operating expenses in 1999.



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##### Table of Contents

We hold an interest in Colloral LLC, which is manufacturing, marketing and selling Colloral, The Collagen Solution and
Vital 3 as dietary supplements, and manufacturing Vital 3 for sale by Futurebiotics LLC and related companies. While we are not contractually committed to make additional capital contributions to Colloral LLC, during the year ended December 31,
2007, we made additional contributions of $12,000 to support continuing marketing efforts related to potential sales through The Shopping Channel in Canada.

No capital contributions were made during the nine months ended September 30, 2008. We may make additional capital contributions to Colloral LLC. Despite any additional investment, there can be no assurance that these efforts will be
successful. Accordingly, in the future we may again incur substantial losses.

Our working capital and capital requirements will depend on numerous
factors, including the strategic direction that we and our shareholders choose, the level of resources that we devote to the development of our patented products, the extent to which we proceed by means of collaborative relationships with
pharmaceutical or nutraceutical companies and our competitive environment. During the nine months ended September 30, 2008, we utilized $95,000 of cash to fund operations. The most significant use of cash for the nine months ended
September 30, 2008 was legal and accounting expenses totaling $231,000. We expect to continue to use our current cash and marketable investments on hand to fund our operations and development efforts. Based upon our budget for calendar year
2008 and current expectations for future years, we believe that current cash and marketable securities, and the interest earned from the investment thereof, will be sufficient to meet our operating expenses and capital requirements for at least the
next five years. At the appropriate time, we may seek additional funding through public or private equity or debt financing, from collaborative arrangements with pharmaceutical companies or from other sources. If additional funds are necessary but
not available, we will have to reduce or not pursue certain activities, which could include areas of research, product development or marketing activity, or otherwise modify our business strategy. Such a reduction would have a material adverse
effect on us.

In order to preserve principal and maintain liquidity, our funds are generally invested in U.S. Treasury obligations and money market
instruments. As of September 30, 2008, our cash and cash equivalents and marketable securities totaled $8,591,000. Current liabilities at September 30, 2008 were $129,000.

Off-Balance Sheet Arrangements

We have not created, and are not party to, any special-purpose or off-balance sheet
entities for the purpose of raising capital, incurring debt or operating parts of our business that are not consolidated into our financial statements. Effective for the third quarter of 2005, we are required to consolidate Colloral LLC, a joint
venture for the development and marketing of dietary supplements.

Recent Accounting Pronouncements

In December 2007, the FASB issued SFAS No. 141R, Business Combinations. SFAS No. 141R, among other aspects, requires the acquiring entity in a
business combination to recognize all (and only) the assets acquired and liabilities assumed in the transaction; establishes the acquisition-date fair value as the measurement objective for all assets acquired and liabilities assumed; and requires
the acquirer to disclose certain information to enable users to understand the nature and financial effect of the business combination. The statement requires that cash outflows such as transaction costs and post-acquisition restructuring be charged
to expense instead of capitalized as a cost of the acquisition. Contingent purchase price will be recorded at its initial fair value and then re-measured as time passes through adjustments to net income. SFAS No. 141R is effective for us in
2009. We are currently evaluating the impact of adoption.

In December 2007, the FASB issued SFAS No. 160, Noncontrolling Interests in
Consolidated Financial Statements. SFAS No. 160 will change the accounting for minority interests, which will be reclassified as noncontrolling interests and classified as a component of equity. SFAS No. 160 is effective for us in
2009. We are currently evaluating the impact of adoption.

In December 2007, the EITF of the FASB reached a consensus on Issue No. 07-1,
Accounting for Collaborative Arrangements. The EITF established the definition of a collaborative arrangement and determined that revenues and costs incurred with third parties in connection with collaborative arrangements would
be presented gross or net based on the criteria in EITF 99-19 and other accounting literature. Based on the nature of the arrangement, payments to or from collaborators would be evaluated and the arrangements terms, the nature of the
entitys business, and whether those payments are within the scope of other accounting literature would be presented. Companies are also required to disclose the nature and purpose of collaborative arrangements along with the accounting
policies and the classification and amounts of significant financial- statement amounts related to the arrangements. Activities in the arrangement conducted in a separate legal entity should be accounted for under other accounting literature;
however required disclosure under EITF 07-1 applies to the entire collaborative agreement. EITF 07-1 is effective for us January 1, 2009 and is to be applied retrospectively to all periods presented for all collaborative arrangements
existing as of the effective date. We do not expect the adoption of EITF 07-1 to have a material impact on our consolidated financial statements.



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Forward-Looking Statements

Statements in this Quarterly Report that are not strictly historical are 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. These statements include statements about our future operating results, strategic relationships and product development. You can identify these forward-looking statements because they involve
our expectations, beliefs, projections, anticipations or other characterizations of future events or circumstances. These forward-looking statements are not guarantees of future performance and are subject to risks and uncertainties that may cause
our actual results to differ significantly from results discussed in the forward-looking statements. These factors include, but are not limited to, our extremely limited operations, the uncertainties of clinical trial results and product development
efforts, our dependence on third parties for licensing and other revenue, our dependence on determinations of regulatory authorities and risks of technological change and competition. These factors are more fully discussed in our most recent Annual
Report on Form 10-KSB filed with the Securities and Exchange Commission in the section Risk Factors. We have no plans, and disclaim any obligation, to update or revise any forward-looking statements whether as a result of new
information, future events or other factors, except as required by law.



|ITEM 3. | QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK
|------- | ----------------------------------------------------------

We have
invested all of our cash in U.S. Government Agency debt securities and money market instruments. These investments are denominated in U.S. dollars. Our exposure to market interest rate risk relates to our cash, cash equivalents and marketable
securities. As of September 30, 2008, our $8,591,000 of cash and cash equivalents consisted of Government agency and treasury money market instruments. Due to the conservative nature of these instruments, we do not believe that a change in
market rates would have a material negative impact on the value of our cash and cash equivalents. Declines of interest rates over time will, however, reduce our interest income from our investments. Interest income was $51,000 and $195,000 for the
three and nine months ended September 30, 2008, respectively.



|ITEM 4. | CONTROLS AND PROCEDURES
|------- | -----------------------

Managements Evaluation of
Disclosure Controls and Procedures

Our Chief Executive Officer and Director of Finance and Treasurer evaluated the effectiveness of our disclosure
controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended) as of September 30, 2008. Based upon this evaluation, our Chief Executive Officer and Director of Finance and Treasurer
concluded that, as of September 30, 2008, our disclosure controls and procedures were effective in providing reasonable assurance that information required to be disclosed in the reports that we file or submit under the Securities Exchange Act
of 1934, as amended, is recorded, processed, summarized and reported, within the time periods specified in the Securities and Exchange Commissions rules and forms.

Changes in Internal Control

There was no change in our internal control over financial reporting (as defined in Rule
13a-15(f) or Rule 15d-15(f) under the Securities Exchange Act of 1934, as amended) during the quarter ended September 30, 2008 that materially affected, or is reasonably likely to materially affect, our internal control over financial
reporting.



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PART IIOTHER INFORMATION



|ITEM 6. | EXHIBITS
|------- | --------

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



|              |  |                                                                                                                      
|------------- |  | ---------------------------------------------------------------------------------------------------------------------
|ExhibitNumber |  | Description                                                                                                          
|31.1          |  | Certification of the Chief Executive Officer pursuant to Exchange Act Rules 13a-14(a)/15d-14(a)                      
|              | 
|31.2          |  | Certification of the Director of Finance and Treasurer pursuant to Exchange Act Rules 13a-14(a)/15d-14(a)            
|              | 
|32.1          |  | Certification of the Chief Executive Officer and Director of Finance and Treasurer pursuant to 18 U.S.C. Section 1350



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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.



|                        |  |                                                
|----------------------- |  | -----------------------------------------------
|                        |  | AUTOIMMUNE INC.                                
|                        | 
|Date: November 13, 2008 |  | /S/ ROBERT C. BISHOP                           
|                        |  | Robert C. Bishop                               
|                        |  | Chairman, President and Chief Executive Officer
|                        | 
|Date: November 13, 2008 |  | /S/ DIANE M.
MCCLINTOCK                        
|                        |  | Diane M. McClintock                            
|                        |  | Director of Finance and Treasurer              



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