##### Table of Contents





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 March 31, 2009



| ̈ | 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 has
submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such
shorter period that the registrant was required to submit and post such files).     ̈  Yes     ̈  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 May 6, 2009:



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









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##### Table of Contents

AUTOIMMUNE INC.

QUARTER ENDED MARCH 31, 2009

TABLE OF CONTENTS



|                                                                                                                                                                                     |  |           
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |  | ----------
|                                                                                                                                                                                     |  | PageNumber
|PART IFINANCIAL INFORMATION                                                                                                                                                         |  |           
|                                                                                                                                                                                     | 
|Item 1Financial Statements (Unaudited)                                                                                                                                              |  |           
|                                                                                                                                                                                     | 
|Consolidated Balance Sheet as of December 31, 2008 and March 31, 2009 (unaudited)                                                                                                    |  | 3         
|                                                                                                                                                                                     | 
|Consolidated Statement of Operations for the three months ended March 
31, 2008 and 2009 and for the period from September 9, 1988 (date of inception) to March 31, 2009 (unaudited) |  | 4         
|                                                                                                                                                                                     | 
|Consolidated Statement of Cash Flows for the three months ended March 
31, 2008 and 2009 and for the period from September 9, 1988 (date of inception) to March 31, 2009 (unaudited) |  | 5         
|                                                                                                                                                                                     | 
|Notes to the Unaudited Consolidated Financial Statements                                                                                                                             |  | 6         
|                                                                                                                                                                                     | 
|Item 2Managements Discussion and Analysis of Financial Condition and Results of
Operations                                                                                         |  | 12        
|                                                                                                                                                                                     | 
|Item 3Quantitative and Qualitative Disclosures about Market Risk                                                                                                                    |  | 14        
|                                                                                                                                                                                     | 
|Item 4Controls and Procedures                                                                                                                                                       |  | 15        
|                                                                                                                                                                                     | 
|PART IIOTHER INFORMATION                                                                                                                                                            |  |           
|                                                                                                                                                                                     | 
|Item 6Exhibits                                                                                                                                                                      |  | 16        
|                                                                                                                                                                                     | 
|Signatures                                                                                                                                                                           |  | 17        



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PART IFINANCIAL INFORMATION



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

AUTOIMMUNE INC.

(A development stage company)

CONSOLIDATED BALANCE SHEET

(Unaudited)



|                                                                                                                                              |  |                  |              |   |               |   |              |  
|--------------------------------------------------------------------------------------------------------------------------------------------- |  | ---------------- | ------------ | - | ------------- | - | ------------ | -
|                                                                                                                                              |  | December 31,2008 |              |   | March 31,2009 |  
|ASSETS                                                                                                                                        |  |                  |              |   |               |   |              |  
|Current assets:                                                                                                                               |  |                  |              |   |               |   |              |  
|Cash and cash equivalents                                                                                                                     |  | $                | 8,475,000    |   |               | $ | 8,463,000    |  
|Marketable securities                                                                                                                         |  |                  |             |   |               |   |             |  
|Accounts receivable                                                                                                                           |  |                  | 37,000       |   |               |   | 53,000       |  
|Prepaid expenses, inventories and other current assets                                                                                        |  |                  | 158,000      |   |               |   | 95,000       |  
|                                                                                                                                              |  |                  |              |   |               |   |              |  
|Total current assets                                                                                                                          |  |                  | 8,670,000    |   |               |   | 8,611,000    |  
|                                                                                                                                              |  |                  |              |   |               |   |              |  
|Total assets                                                                                                                                  |  | $                | 8,670,000    |   |               | $ | 8,611,000    |  
|                                                                                                                                              |  |                  |              |   |               |   |              |  
|                                                                                                                                              |  |                 
|LIABILITIES AND STOCKHOLDERS EQUITY                                                                                                          |  |                  |              |   |               |   |              |  
|Current liabilities:                                                                                                                          |  |                  |              |   |               |   |              |  
|Accounts payable                                                                                                                              |  | $                | 18,000       |   |               | $ | 116,000      |  
|Accrued professional fees                                                                                                                     |  |                  | 110,000      |   |               |   | 91,000       |  
|Deferred revenue                                                                                                                              |  |                  | 19,000       |   |               |   | 21,000       |  
|                                                                                                                                              |  |                  |              |   |               |   |              |  
|Total current liabilities                                                                                                                     |  |                  | 147,000      |   |               |   | 228,000      |  
|                                                                                                                                              |  |                  |              |   |               |   |              |  
|Commitments and contingencies                                                                                                                 |  |                  |              |   |               |   |              |  
|Stockholders equity:                                                                                                                         |  |                  |              |   |               |   |              |  
|Preferred stock, $0.01 par value: 5,000,000 shares authorized; no shares issued and outstanding at December 31, 2008 and March 31,
2009       |  |                  |             |   |               |   |             |  
|Common stock, $0.01 par value; 25,000,000 shares authorized; 16,999,623 shares issued and outstanding at December 31, 2008 and
March 31, 2009 |  |                  | 170,000      |   |               |   | 170,000      |  
|Additional paid-in capital                                                                                                                    |  |                  | 118,426,000  |   |               |   | 118,450,000  |  
|Deficit accumulated during the development stage                                                                                              |  |                  | (110,106,000 | ) |               |   | (110,276,000 | )
|                                                                                                                                              |  |                  |              |   |               |   |              |  
|Total AutoImmune shareholders equity                                                                                                         |  |                  | 8,490,000    |   |               |   | 8,344,000    |  
|Noncontrolling interest                                                                                                                       |  |                  | 33,000       |   |               |   | 39,000       |  
|                                                                                                                                              |  |                  |              |   |               |   |              |  
|Total equity                                                                                                                                  |  |                  | 8,523,000    |   |               |   | 8,383,000    |  
|                                                                                                                                              |  |                  |              |   |               |   |              |  
|Total liabilities and equity                                                                                                                  |  | $                | 8,670,000    |   |               | $ | 8,611,000    |  
|                                                                                                                                              |  |                  |              |   |               |   |              |  

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 |            |               | Period fromSeptember 9, 1988(date of inception)toMarch 31, 2009 |  
|                                                                | March 31,2008 |                    |            | March 31,2009 |                                                                 |  
|Revenue:                                                        |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|License rights                                                  |               | $                  | 45,000     |               |                                                                 | $ | 45,000     |   |  | $ | 7,748,000    |  
|Option fees                                                     |               |                    | 1,000      |               |                                                                 |   |           |   |  |   | 2,214,000    |  
|Research and development revenue under collaborative agreements |               |                    |           |               |                                                                 |   |           |   |  |   | 955,000      |  
|Product revenue                                                 |               |                    | 21,000     |               |                                                                 |   | 59,000     |   |  |   | 535,000      |  
|                                                                |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Total revenue                                                   |               |                    | 67,000     |               |                                                                 |   | 104,000    |   |  |   | 11,452,000   |  
|                                                                |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Costs and expenses:                                             |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Cost of product revenue                                         |               |                    | 12,000     |               |                                                                 |   | 20,000     |   |  |   | 136,000      |  
|Research and development:                                       |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Related party                                                   |               |                    | 3,000      |               |                                                                 |   | 3,000      |   |  |   | 20,010,000   |  
|All other                                                       |               |                    | 39,000     |               |                                                                 |   | 68,000     |   |  |   | 93,020,000   |  
|Selling, general and administrative                             |               |                    | 205,000    |               |                                                                 |   | 188,000    |   |  |   | 22,288,000   |  
|                                                                |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Total costs and expenses                                        |               |                    | 259,000    |               |                                                                 |   | 279,000    |   |  |   | 135,454,000  |  
|                                                                |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Total operating loss                                            |               |                    | (192,000   | )             |                                                                 |   | (175,000   | ) |  |   | (124,002,000 | )
|                                                                |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Interest income                                                 |               |                    | 84,000     |               |                                                                 |   | 9,000      |   |  |   | 14,333,000   |  
|Interest expense                                                |               |                    |           |               |                                                                 |   |           |   |  |   | (303,000     | )
|Equity in net loss of unconsolidated affiliate                  |               |                    |           |               |                                                                 |   |           |   |  |   | (250,000     | )
|Other income (expense)                                          |               |                    |           |               |                                                                 |   |           |   |  |   | (50,000      | )
|                                                                |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Net loss                                                        |               | $                  | (108,000   | )             |                                                                 | $ | (166,000   | ) |  | $ | (110,272,000 | )
|Less: Net income (loss) attributable to noncontrolling interest |               |                    | (1,000     | )             |                                                                 |   | 4,000      |   |  |   |             |  
|                                                                |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Net loss attributable to AutoImmune Inc                         |               | $                  | (107,000   | )             |                                                                 | $ | (170,000   | ) |  | $ | (110,272,000 | )
|                                                                |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Net loss per share-basic                                        |               | $                  | (0.01      | )             |                                                                 | $ | (0.01      | ) |  |   |              |  
|                                                                |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Net loss per share-diluted                                      |               | $                  | (0.01      | )             |                                                                 | $ | (0.01      | ) |  |   |              |  
|                                                                |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Weighted average common shares outstanding-basic                |               |                    | 16,997,205 |               |                                                                 |   | 16,999,623 |   |  |   |              |  
|                                                                |               |                    |            |               |                                                                 |   |            |   |  |   |              |  
|Weighted average common shares outstanding-diluted              |               |                    | 16,997,205 |               |                                                                 |   | 16,999,623 |   |  |   |              |  
|                                                                |               |                    |            |               |                                                                 |   |            |   |  |   |              |  

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)



|                                                                                                                    |               |                    |           |               |                                                                 |   |           |   |  |   |              |  
|------------------------------------------------------------------------------------------------------------------- | ------------- | ------------------ | --------- | ------------- | --------------------------------------------------------------- | - | --------- | - |  | - | ------------ | -
|                                                                                                                    |               | Three months ended |           |               | Period fromSeptember 9, 1988(date of inception)toMarch 31, 2009 |  
|                                                                                                                    | March 31,2008 |                    |           | March 31,2009 |                                                                 |  
|Cash flows from operating activities:                                                                               |               |                    |           |               |                                                                 |   |           |   |  |   |              |  
|Net loss                                                                                                            |               | $                  | (108,000  | )             |                                                                 | $ | (166,000  | ) |  | $ | (110,272,000 | )
|Adjustment to reconcile net loss to net cash used by operating activities:                                          |               |                    |           |               |                                                                 |   |           |   |  |   |              |  
|Interest expense related to demand notes converted into Series A mandatorily redeemable 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                                                                                          |               |                    | 31,000    |               |                                                                 |   | 24,000    |   |  |   | 276,000      |  
|Noncash contributions to joint venture from noncontrolling interest                                                 |               |                    | 2,000     |               |                                                                 |   | 2,000     |   |  |   | 39,000       |  
|Depreciation and amortization                                                                                       |               |                    |          |               |                                                                 |   |          |   |  |   | 4,464,000    |  
|Loss on sale/disposal of fixed assets                                                                               |               |                    |          |               |                                                                 |   |          |   |  |   | 642,000      |  
|Noncash interest income                                                                                             |               |                    |          |               |                                                                 |   |          |   |  |   | (3,000       | )
|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                                                                          |               |                    | (13,000   | )             |                                                                 |   | (16,000   | ) |  |   | (53,000      | )
|(Increase) decrease in prepaid expenses and other current assets                                                    |               |                    | 41,000    |               |                                                                 |   | 63,000    |   |  |   | (95,000      | )
|Increase (decrease) in accounts payable                                                                             |               |                    | 25,000    |               |                                                                 |   | 98,000    |   |  |   | 116,000      |  
|Increase (decrease) in accrued expenses                                                                             |               |                    | 6,000     |               |                                                                 |   | (19,000   | ) |  |   | 71,000       |  
|Increase (decrease) in deferred revenue                                                                             |               |                    | 2,000     |               |                                                                 |   | 2,000     |   |  |   | 21,000       |  
|                                                                                                                    |               |                    |           |               |                                                                 |   |           |   |  |   |              |  
|Net cash used by operating activities                                                                               |               |                    | (14,000   | )             |                                                                 |   | (12,000   | ) |  |   | (103,483,000 | )
|                                                                                                                    |               |                    |           |               |                                                                 |   |           |   |  |   |              |  
|Cash flows from investing activities:                                                                               |               |                    |           |               |                                                                 |   |           |   |  |   |              |  
|Purchase of available-for-sale marketable securities                                                                |               |                    |          |               |                                                                 |   |          |   |  |   | (322,315,000 | )
|Proceeds from sale/maturity of available-for-sale marketable securities                                             |               |                    |          |               |                                                                 |   |          |   |  |   | 311,307,000  |  
|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     | )
|Increase in patent costs                                                                                            |               |                    |          |               |                                                                 |   |          |   |  |   | (563,000     | )
|Increase in other assets                                                                                            |               |                    |          |               |                                                                 |   |          |   |  |   | (125,000     | )
|                                                                                                                    |               |                    |           |               |                                                                 |   |           |   |  |   |              |  
|Net cash used by investing activities                                                                               |               |                    |          |               |                                                                 |   |          |   |  |   | (5,997,000   | )
|                                                                                                                    |               |                    |           |               |                                                                 |   |           |   |  |   |              |  
|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                                                                              |               |                    | 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 by financing activities                                                                           |               |                    | (115,000  | )             |                                                                 |   |          |   |  |   | 117,943,000  |  
|                                                                                                                    |               |                    |           |               |                                                                 |   |           |   |  |   |              |  
|Net increase (decrease) in cash and cash equivalents                                                                |               |                    | (129,000  | )             |                                                                 |   | (12,000   | ) |  |   | 8,463,000    |  
|Cash and cash equivalents, beginning of period                                                                      |               |                    | 7,994,000 |               |                                                                 |   | 8,475,000 |   |  |   |             |  
|                                                                                                                    |               |                    |           |               |                                                                 |   |           |   |  |   |              |  
|Cash and cash equivalents, end of period                                                                            |               | $                  | 7,865,000 |               |                                                                 | $ | 8,463,000 |   |  | $ | 8,463,000    |  
|                                                                                                                    |               |                    |           |               |                                                                 |   |           |   |  |   |              |  

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 March 31, 2009, for the three months ended March 31, 2008 and 2009 and for the period from inception (September 9, 1988) through March 31, 2009 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, 2008 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, 2008 included in our Form 10-K. 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 $31,000 and $24,000 for the three months ended
March 31, 2008 and 2009, respectively and is recorded as selling, general and administrative expense in the accompanying consolidated statement of operations.

The fair value of each option grant is estimated on the date of grant using the Black-Scholes option pricing model with the following weighted average assumptions used for grants in the three months ended
March 31, 2008 and 2009:



|                                |  |                              |   |  |                    |  
|------------------------------- |  | ---------------------------- | - |  | ------------------ | -
|                                |  | Three months ended March 31, |  
|                                |  | 2008                         |   |  | 2008               |  
|Risk free interest rate range   |  | 2.67% to 3.1                 | % |  | 1.11% to 2.28      | %
|Expected range of life in years |  | 3 years to 6 years           |   |  | 3 years to 6 years |  
|Expected volatility             |  | 75                           | % |  | 55% to 72          | %
|Expected dividends              |  |                             |   |  |                   |  

Estimates of fair value are not intended to predict actual future events or the value ultimately
realized by persons who receive equity awards.



|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 assumed outstanding during the period. For the three months ended March 31, 2008 and 2009, shares used to compute diluted earnings per share excluded 1,167,000 and 1,204,500 stock options, respectively, as their
inclusion would have been anti-dilutive due to the net losses incurred in these years.



|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. The adoption of SFAS 157 for 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 March 31, 2009 and December 31, 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:



|                 |  |                  |           |                                        |   |                                           |  |                                        |   |  |   |  
|---------------- |  | ---------------- | --------- | -------------------------------------- | - | ----------------------------------------- |  | -------------------------------------- | - |  | - | -
|                 |  | March 31,2009    |           | Quoted Pricesin ActiveMarkets(Level 1) |   | SignificantOtherObservableInputs(Level 2) |  | SignificantUnobservableInputs(Level 3)
|Assets:          |  |                  |           |                                        |   |                                           |  |                                        |   |  |   |  
|Cash equivalents |  | $                | 8,157,000 |                                        | $ | 8,157,000                                 |  | $                                      |  |  | $ | 
|                 |  |                  |           |                                        |   |                                           |  |                                        |   |  |   |  
|Total            |  | $                | 8,157,000 |                                        | $ | 8,157,000                                 |  | $                                      |  |  | $ | 
|                 |  |                  |           |                                        |   |                                           |  |                                        |   |  |   |  
|                 |  |                  |           |                                       
|                 |  | December 31,2008 |           | Quoted Pricesin ActiveMarkets(Level 1) |   | SignificantOtherObservableInputs(Level 2) |  | SignificantUnobservableInputs(Level 3)
|Assets:          |  |                  |           |                                        |   |                                           |  |                                        |   |  |   |  
|Cash equivalents |  | $                | 8,206,000 |                                        | $ | 8,206,000                                 |  | $                                      |  |  | $ | 
|                 |  |                  |           |                                        |   |                                           |  |                                        |   |  |   |  
|Total            |  | $                | 8,206,000 |                                        | $ | 8,206,000                                 |  | $                                      |  |  | $ | 
|                 |  |                  |           |                                        |   |                                           |  |                                        |   |  |   |  

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.

Effective this quarter, we implemented
Statement of Financial Accounting Standards No. 157, Fair Value Measurements, or SFAS 157, for our non-financial assets and liabilities that are remeasured at fair value on a non-recurring basis. The adoption of SFAS 157 for our
non-financial assets and liabilities that are remeasured at fair value on a non-recurring basis did not impact our financial position or results of operations; however, could have an impact in future periods. In addition, we may have additional
disclosure requirements in the event we complete an acquisition or incur impairment of our assets in future periods.



|5. | Cash Equivalents
|-- | ----------------

Cash equivalents are carried at
cost which approximated fair value at December 31, 2008 and March 31, 2009, and were primarily invested in money market accounts. We did not hold any available-for-sale marketable securities at March 31, 2009.

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
|-- | ------------

In January 2003, the FASB issued FIN
46 and, in December 2003, the FASB issued FIN 46R. FIN 46R replaces FIN 46 and addresses consolidation by business enterprises of variable interest entities that possess certain characteristics. A variable interest entity is an entity that does not
have sufficient equity investment to permit it to finance its activities without additional financial support from a third party, or whose equity investors lack the characteristics of a controlling financial interest. FIN 46R establishes standards
for determining under what circumstances variable interest entities should be consolidated with their primary beneficiary. We adopted FIN 46R in the first quarter of 2004 for non-special purpose entities created prior to February 1, 2003. The
adoption of FIN 46R did not have an initial material effect on our financial condition or results of operations. We now evaluate all transactions and relationships with potential variable interest entities (VIEs) in accordance with FIN 46R.

Our overall methodology for evaluating transactions and relationships under FIN 46R includes the following:



| |  |  | determining whether the entity is a VIE, and, if so,
| | - |  | ----------------------------------------------------



| |  |  | determining whether we are the primary beneficiary of the VIE.
| | - |  | --------------------------------------------------------------



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##### Table of Contents

In performing the first step, the significant factors and judgments that we consider include:



| |  |  | the design of the entity, including the nature of its risks and the purpose for which the entity was created, to determine the variability that the entity was
designed to create and distribute to its interest holders,
| | - |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | the nature of our involvement with the entity,
| | - |  | ----------------------------------------------



| |  |  | whether control of the entity results through arrangements that do not involve voting equity,
| | - |  | ---------------------------------------------------------------------------------------------



| |  |  | whether there is sufficient equity investment at risk to finance the activities of the entity, and
| | - |  | --------------------------------------------------------------------------------------------------



| |  |  | whether parties other than the equity holders have the obligation to absorb expected losses or the right to receive expected residual returns.
| | - |  | ----------------------------------------------------------------------------------------------------------------------------------------------

For each VIE identified, we evaluate whether we are the primary beneficiary of the VIE by considering:



| |  |  | whether our variable interest absorbs the majority of the VIEs expected losses,
| | - |  | --------------------------------------------------------------------------------



| |  |  | whether our variable interest receives the majority of the VIEs expected residual returns, and
| | - |  | -----------------------------------------------------------------------------------------------



| |  |  | whether we have the ability to make decisions that significantly affect the VIEs results and activities.
| | - |  | ---------------------------------------------------------------------------------------------------------

Based on our evaluation of the above factors and judgments, as of March 31, 2009, we consolidate one VIE, Colloral LLC, of which we are the primary
beneficiary.

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 is greater than 50% and we actively participate in its management, but
we do not have voting control of Colloral LLC. Therefore, the investment had historically been accounted for using the equity method. Upon adoption of FIN 46R our interest in Colloral LLC did not qualify as a variable interest entity and therefore
we continued to account for our investment in Colloral LLC under the equity method of accounting until August 2005. 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, Colloral LLC is considered a variable
interest entity, of which we are the primary beneficiary. We are required to consolidate Colloral LLC for financial reporting purposes in accordance with FIN 46R, effective in the third quarter of 2005. 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 agreements, 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 $1,032,000 to Colloral LLC from 2003
through 2007. We satisfied our funding commitment in 2006 and have made no capital contributions during the year ended December 31, 2008 or the three months ended March 31, 2009. 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.

At December 31, 2008 and March 31, 2009, the excess of Deserets capital contributions over their portion of the accumulated losses is
recorded as a noncontrolling interest in our consolidated balance sheet.



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##### Table of Contents

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, 2008 and March 31, 2009 and Colloral LLCs operating results for the three months ended March 31, 2008 and 2009 have been consolidated into our
financial statements:



|                                            |  |                              |         |   |      |   |       
|------------------------------------------- |  | ---------------------------- | ------- | - | ---- | - | ------
|                                            |  | Three months ended March 31,
|                                            |  | 2008                         |         |   | 2009
|Statement of Operations Data:               |  |                              |         |   |      |   |       
|Revenue                                     |  | $                            | 22,000  |   |      | $ | 59,000
|Cost of goods sold                          |  |                              | 12,000  |   |      |   | 20,000
|Selling, general and administrative expense |  |                              | 27,000  |   |      |   | 24,000
|Net income (loss)                           |  | $                            | (17,000 | ) |      | $ | 15,000



|                      |  |                  |         |               |   |        
|--------------------- |  | ---------------- | ------- | ------------- | - | -------
|                      |  | December 31,2008 |         | March 31,2009
|Balance Sheet Data:   |  |                  |         |               |   |        
|Current assets        |  | $                | 219,000 |               | $ | 255,000
|Long term assets      |  |                  |        |               |   |       
|Current liabilities   |  |                  | 6,000   |               |   | 24,000 
|Long term liabilities |  |                  |        |               |   |       

As of December 31, 2008 and March 31, 2009, respectively, current liabilities included $0 and
$16,000, respectively, payable to Deseret, a related party.

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 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.

Effective January 1, 2009, we implemented Statement of Financial Accounting Standards No. 160, Noncontrolling Interests in Consolidated
Financial Statements, an amendment to ARB No. 51, or SFAS 160. SFAS No. 160 changed the accounting for minority interests, which will be reclassified as noncontrolling interests and classified as a component of equity. The adoption of
SFAS 160 has resulted in the reclassification of amounts previously attributable to minority interest (now referred to as noncontrolling interest) to a separate component of Shareholders Equity on the accompanying consolidated balance sheet.
Additionally, net income attributable to noncontrolling interests is shown separately from net income in the consolidated statements of income. Finally, the net loss reflected on the statement of cash flows is the consolidated net loss. This
reclassification had no effect on our previously reported financial position or results of operations.

Prior year amounts related to
noncontrolling interest (previously referred to as minority interest) have been reclassified to conform to the current year presentation as required by SFAS 160.



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##### Table of Contents

The following table presents a reconciliation of the changes in equity during the three months ended
March 31, 2008 and 2009:



|                                           |  |                              |           |   |                        |   |        |       |  |   |                      |   |  |                        |           |       |  |   |        |  |   |           |  
|------------------------------------------ |  | ---------------------------- | --------- | - | ---------------------- | - | ------ | ----- |  | - | -------------------- | - |  | ---------------------- | --------- | ----- |  | - | ------ |  | - | --------- | -
|                                           |  | Three months ended March 31, |          
|                                           |  | 2008                         |           |   | 2009                   |  
|                                           |  | AutoImmunesInterest         |           |   | NoncontrollingInterest |   |        | Total |  |   | AutoImmunesInterest |   |  | NoncontrollingInterest |           | Total | 
|Balance at the beginning of the period     |  | $                            | 8,832,000 |   |                        | $ | 11,000 |       |  | $ | 8,843,000            |   |  | $                      | 8,490,000 |       |  | $ | 33,000 |  | $ | 8,523,000 |  
|Net income (loss)                          |  |                              | (107,000  | ) |                        |   | (1,000 | )     |  |   | (108,000             | ) |  |                        | (170,000  | )     |  |   | 4,000  |  |   | (166,000  | )
|Stock-based employee compensation          |  |                              | 31,000    |   |                        |   |       |       |  |   | 31,000               |   |  |                        | 24,000    |       |  |   |       |  |   | 24,000    |  
|Issuance of common shares                  |  |                              | 10,000    |   |                        |   |       |       |  |   | 10,000               |   |  |                        |          |       |  |   |       |  |   |          |  
|Repurchase of outstanding warrants         |  |                              | (125,000  | ) |                        |   |       |       |  |   | (125,000             | ) |  |                        |          |       |  |   |       |  |   |          |  
|Contributions from noncontrolling interest |  |                              |          |   |                        |   | 3,000  |       |  |   | 3,000                |   |  |                        |          |       |  |   | 2,000  |  |   | 2,000     |  
|Other comprehensive income (loss)          |  |                              | 4,000     |   |                        |   |       |       |  |   | 4,000                |   |  |                        |          |       |  |   |       |  |   |          |  
|                                           |  |                              |           |   |                        |   |        |       |  |   |                      |   |  |                        |           |       |  |   |        |  |   |           |  
|                                           |  |                              |           |   |                        |  
|Balance at the end of the period           |  | $                            | 8,645,000 |   |                        | $ | 13,000 |       |  | $ | 8,658,000            |   |  | $                      | 8,344,000 |       |  | $ | 39,000 |  | $ | 8,383,000 |  
|                                           |  |                              |           |   |                        |   |        |       |  |   |                      |   |  |                        |           |       |  |   |        |  |   |           |  



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

The
components of comprehensive loss, none of which is attributable to the noncontrolling interest, consisted of the following:



|                                                |  |                                     |          |   |      |   |          |  
|----------------------------------------------- |  | ----------------------------------- | -------- | - | ---- | - | -------- | -
|                                                |  | For the three monthsended March 31, |         
|                                                |  | 2008                                |          |   | 2009 |  
|Net income (loss)                               |  | $                                   | (107,000 | ) |      | $ | (170,000 | )
|Change in unrealized gain (loss) on investments |  |                                     | 4,000    |   |      |   |         |  
|                                                |  |                                     |          |   |      |   |          |  
|Comprehensive income (loss)                     |  | $                                   | (103,000 | ) |      | $ | (170,000 | )
|                                                |  |                                     |          |   |      |   |          |  



|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. | New Accounting Pronouncements
|--- | -----------------------------

Effective
January 1, 2009, we implemented Statement of Financial Accounting Standards No. 160, Noncontrolling Interests in Consolidated Financial Statements, an amendment to ARB No. 51, or SFAS 160. This standard changed the accounting
for and reporting of minority interest (now called noncontrolling interest) in our consolidated financial statements. Upon adoption, certain prior period amounts have been reclassified to conform to the current period financial statement
presentation. These reclassifications have no effect on our previously reported financial position or results of operations. Refer to Note 6 of this Form 10-Q for additional information on the adoption of SFAS 160.



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##### Table of Contents

Effective January 1, 2009, we implemented 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. Due to the fact that SFAS 141(R) is applicable to future acquisitions completed after January 1, 2009 and we did not have any business combinations this quarter, the adoption of SFAS 141(R) did not have
an impact on our consolidated financial statements.

Effective January 1, 2009, we implemented EITF 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. The adoption of EITF 07-01 did not have an impact on our consolidated financial statements.

Recent Accounting Pronouncements

In April 2009, the FASB issued the following new accounting interpretations. These
standards are effective for periods ending after June 15, 2009. We are evaluating the impact that these standards will have on our financial statements:



| |  |  | FASB Staff Position FAS 157-4, Determining Whether a Market Is Not Active and a Transaction Is Not Distressed,or FSP FAS 157-4; FSP FAS 157-4 provides
guidelines for making fair value measurements more consistent with the principles presented in SFAS 157. FSP FAS 157-4 provides additional authoritative guidance in determining whether a market is active or inactive, and whether a transaction is
distressed, is applicable to all assets and liabilities (i.e. financial and nonfinancial) and will require enhanced disclosures.
| | - |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | FASB Staff Position FAS 115-2, FAS 124-2, and EITF 99-20-2, Recognition and Presentation of Other-Than-Temporary Impairments, or FSP FAS 115-2, FAS 124-2,
and EITF 99-20-2; and FSP FAS 115-2, FAS 124-2, and EITF 99-20-2 provides additional guidance to provide greater clarity about the credit and noncredit component of an other-than-temporary impairment event and to more effectively communicate when an
other-than-temporary impairment event has occurred. This FSP applies to debt securities.
| | - |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | FASB Staff Position FAS 107-1 and APB 28-1, Interim Disclosures about Fair Value of Financial Instruments, or FSP FAS 107-1 and APB 28-1. FSP FAS 107-1 and
APB 28-1, amends FASB Statement No. 107, Disclosures about Fair Value of Financial Instruments, to require disclosures about fair value of financial instruments in interim as well as in annual financial statements. This FSP also amends
APB Opinion No. 28, Interim Financial Reporting, to require those disclosures in all interim 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 March 31, 2009, we have incurred ongoing losses from operations and have cumulative losses as of March 31, 2009 totaling $110,272,000. 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 March 31, 2009 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 is greater than 50% and we actively participate in its management, but we do not have voting control of Colloral LLC. 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, Colloral LLC is now considered a variable interest entity, of which we are the primary beneficiary. We have consolidated Colloral LLC in accordance with FIN 46R, effective
since the third quarter of 2005.

In accordance with the amendment to the Colloral LLC operating agreement, we made additional capital contributions of
$1,032,000 to Colloral LLC from 2003 through 2007. We satisfied our funding commitment in 2006 and have made no capital contributions during the year ended December 31, 2008 or the three months ended March 31, 2009. 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.

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, 2008 and March 31, 2009 and Colloral LLCs operating results for the three months ended March 31, 2008 and 2009 have been consolidated into our financial statements:



|                                            |  |                              |         |   |               |   |        
|------------------------------------------- |  | ---------------------------- | ------- | - | ------------- | - | -------
|                                            |  | Three months ended March 31,
|                                            |  | 2008                         |         |   | 2009         
|Statement of Operations Data:               |  |                              |         |   |               |   |        
|Revenue                                     |  | $                            | 22,000  |   |               | $ | 59,000 
|Cost of goods sold                          |  |                              | 12,000  |   |               |   | 20,000 
|Selling, general and administrative expense |  |                              | 27,000  |   |               |   | 24,000 
|Net income (loss)                           |  | $                            | (17,000 | ) |               | $ | 15,000 
|                                            |  |                             
|                                            |  | December 31,2008             |         |   | March 31,2009
|Balance Sheet Data:                         |  |                              |         |   |               |   |        
|Current assets                              |  | $                            | 219,000 |   |               | $ | 255,000
|Long term assets                            |  |                              |        |   |               |   |       
|Current liabilities                         |  |                              | 6,000   |   |               |   | 24,000 
|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 Months Ended March 31, 2008 and 2009

Revenue was $67,000
and $104,000 for the three months ended March 31, 2008 and 2009, respectively. The revenue in the three months ended March 31, 2008 and 2009 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, whose results are consolidated with ours. From 2006 through January 2009, 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
revenue of $0 and $37,000 during the three months ended March 31, 2008 and 2009, 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 $11,000 and $15,000 during three months ended March 31, 2008 and 2009, 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 $12,000 and $20,000 for the three months ended March 31, 2008 and 2009,
respectively. Fluctuations in cost of good sold are related to the mix of product revenues to consumers versus distributors. Cost of goods sold in three months ended March 31, 2008 was higher as percentage of product revenues due to the
write-off of expired inventory.

Research and development expenses were $42,000 and $71,000 for the three months ended March 31, 2008 and 2009,
respectively. The increase is due to an increase in the patent annuities and legal fees to acquire our international patents.

Selling, general and
administrative expenses were $205,000 and $188,000 for the three months ended March 31, 2008 and 2009, respectively. The decrease is primarily the result of a decrease in the stock compensation costs from $31,000 during the three months ended
March 31, 2008 to $24,000 during the three months ended March 31, 2009 and decrease in management compensation costs of $11,000.

Interest income
was $84,000 and $9,000 for the three months ended March 31, 2008 and 2009, respectively. The decrease is due to a lower average return on investment and a lower average balance of cash and marketable securities available for investment.

Minority interest in joint venture was $1,000 and ($4,000) for the three months ended March 31, 2008 and 2009, respectively. The minority interest in
joint venture reflects Deserets share of Colloral LLCs profits or losses calculated in accordance with the amended terms of the Colloral LLC operating agreement.

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.

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, we may elect to do so. 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 three months ended March 31, 2009, our cash deceased $12,000. The decrease in cash to fund operations. The most



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significant uses of cash for the three months ended March 31, 2009 were legal and accounting expenses totaling $135,000. The most significant source of
cash for the three months ended March 31, 2009 were product and license revenues of $104,000. 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 2009 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 March 31, 2009, our cash and cash equivalents totaled $8,463,000. Current liabilities at March 31, 2009 were $228,000.

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 April 2009, the FASB issued the following new accounting standards. These standards are effective for periods ending after June 15, 2009. We are evaluating the impact that these standards will have on our
financial statements:



| |  |  | FASB Staff Position FAS 157-4, Determining Whether a Market Is Not Active and a Transaction Is Not Distressed,or FSP FAS 157-4; FSP FAS 157-4 provides
guidelines for making fair value measurements more consistent with the principles presented in SFAS 157. FSP FAS 157-4 provides additional authoritative guidance in determining whether a market is active or inactive, and whether a transaction is
distressed, is applicable to all assets and liabilities (i.e. financial and nonfinancial) and will require enhanced disclosures
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | FASB Staff Position FAS 115-2, FAS 124-2, and EITF 99-20-2, Recognition and Presentation of Other-Than-Temporary Impairments, or FSP FAS 115-2, FAS 124-2,
and EITF 99-20-2; and FSP FAS 115-2, FAS 124-2, and EITF 99-20-2 provides additional guidance to provide greater clarity about the credit and noncredit component of an other-than-temporary impairment event and to more effectively communicate when an
other-than-temporary impairment event has occurred. This FSP applies to debt securities.
| | - |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | FASB Staff Position FAS 107-1 and APB 28-1, Interim Disclosures about Fair Value of Financial Instruments, or FSP FAS 107-1 and APB 28-1. FSP FAS 107-1 and
APB 28-1, amends FASB Statement No. 107, Disclosures about Fair Value of Financial Instruments, to require disclosures about fair value of financial instruments in interim as well as in annual financial statements. This FSP also amends
APB Opinion No. 28, Interim Financial Reporting, to require those disclosures in all interim financial statements.
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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-K 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 March 31, 2009, our $8,463,000 of cash and cash equivalents consisted of Government agency and treasury money market



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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 $9,000 for the three months ended March 31, 2009, down from $84,000 for the
three months ended March 31, 2008. A 1% change in interest rates could affect our annual interest income by approximately $85,000.



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

Managements Evaluation of
Disclosure Controls and Procedures

The Companys management, consisting of our Chief Executive Officer and Director of Finance and Treasurer
evaluated the effectiveness of the design and operation 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 March 31, 2009. Based upon this
evaluation, our Chief Executive Officer and Director of Finance and Treasurer concluded that, as of March 31, 2009, 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 March 31, 2009 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: May 13, 2009 |  | /S/ ROBERT C. BISHOP                           
|                   |  | Robert C. Bishop                               
|                   |  | Chairman, President and Chief Executive Officer
|                   | 
|Date: May 13, 2009 |  | /S/ DIANE M.
MCCLINTOCK                        
|                   |  | Diane M. McClintock                            
|                   |  | Director of Finance and Treasurer              



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