##### Table of Contents



UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 
 FORM 10-Q
 (Mark One)
 þ
    
    QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the quarterly period ended September 30, 2009
 or
 o
    
    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the transition period from  to
 Commission file number: 001-33882
 ONCOTHYREON INC.
 (Exact name of registrant as specified in its charter)
 Delaware(State or other jurisdiction of 
incorporation or organization)
    
    26-0868560(I.R.S. Employer
Identification Number)2601 Fourth Ave., Suite 500
Seattle, Washington(Address of principal executive offices)
    
    98121(Zip Code)
 (206) 801-2100  (Registrants telephone number, including area code)
 þ o
 o o
  Large accelerated filer o
Accelerated filer o
Non-accelerated filer þ(Do not check if a smaller reporting company)
Smaller reporting company o o þ




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##### 



ONCOTHYREON INC.
FORM 10-Q FOR THE QUARTER ENDED SEPTEMBER 30, 2009
 INDEX
 PagePart I  Financial Information
    
    
    3Item 1. Financial Statements (unaudited)
    
    
    3Condensed Consolidated Balance Sheets
    
    
    3Condensed Consolidated Statements of Operations and Comprehensive Loss
    
    
    4Condensed Consolidated Statements of Stockholders Equity
    
    
    5Condensed Consolidated Statements of Cash Flows
    
    
    6Notes to the Condensed Consolidated Financial Statements
    
    
    7Item 2. Managements Discussion and Analysis of Financial Condition and Results of Operations
    
    
    12Item 3. Quantitative and Qualitative Disclosures About Market Risk
    
    
    22Item 4. Controls and Procedures
    
    
    22Part II  Other Information
    
    
    23Item 1. Legal Proceedings
    
    
    23Item 1A. Risk Factors
    
    
    23Item 6. Exhibits
    
    
    37Signatures
    
    
    38EX-12.1EX-31.1EX-31.2EX-32.1EX-32.2
   2




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##### Table of Contents



PART I  FINANCIAL INFORMATION
 
 Item 1. Financial Statements (unaudited)
 
 ONCOTHYREON INC.
Condensed Consolidated Balance Sheets
(in thousands, except share amounts)
(Unaudited)
 September 30,
    
    
    December 31,2009
    
    
    2008ASSETSCurrentCash and cash equivalents
    
    $
    34,980
    
    
    $
    19,166Accounts receivable
    
    
    22
    
    
    
    1,828Government grant receivable
    
    
    156
    
    
    
    40Note receivable
    
    
    74
    
    
    
    Prepaid expenses
    
    
    281
    
    
    
    38435,513
    
    
    
    21,418Plant and equipment, net
    
    
    1,493
    
    
    
    867Note receivable
    
    
    148
    
    
    
    215Long term deposit
    
    
    354
    
    
    
    354Goodwill
    
    
    2,117
    
    
    
    2,117$
    39,625
    
    
    $
    24,971LIABILITIESCurrentAccounts payable and accrued expenses
    
    $
    2,368
    
    
    $
    3,843Current portion of deferred revenue
    
    
    18
    
    
    
    182,386
    
    
    
    3,861Notes payable
    
    
    199
    
    
    
    199Deferred revenue
    
    
    153
    
    
    
    164Warrant liability
    
    
    9,921
    
    
    
    Class UA preferred stock, 12,500 shares authorized, 12,500 and 12,500 shares issued and outstanding
    
    
    30
    
    
    
    3012,689
    
    
    
    4,254Contingencies, commitments, and guaranteesSTOCKHOLDERS EQUITYPreferred stock, $0.0001 par value; 10,000,000 shares authorized, no shares issued and outstanding
    
    
    
    
    
    
    Common stock, $0.0001 par value; 100,000,000 shares authorized, 25,661,905 and 19,492,432 shares
issued and outstanding
    
    
    345,105
    
    
    
    325,043Warrants
    
    
    64
    
    
    
    64Additional paid-in capital
    
    
    15,999
    
    
    
    15,094Accumulated deficit
    
    
    (329,166
    )
    
    
    (314,418
    )Accumulated other comprehensive loss
    
    
    (5,066
    )
    
    
    (5,066
    )26,936
    
    
    
    20,717$
    39,625
    
    
    $
    24,971
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##### Table of Contents



ONCOTHYREON INC.
 
 Condensed Consolidated Statements of Operations and Comprehensive Loss
(in thousands, except share and per share amounts)
(Unaudited)
 Three months
    
    
    Nine monthsended September 30,
    
    
    ended September 30,2009
    
    
    2008
    
    
    2009
    
    
    2008RevenueContract manufacturing
    
    $
    
    
    
    $
    426
    
    
    $
    
    
    
    $
    2,946Licensing revenue from collaborative agreements
    
    
    4
    
    
    
    376
    
    
    
    12
    
    
    
    1,028Licensing, royalties, and other revenue
    
    
    
    
    
    
    
    
    
    
    27
    
    
    
    4
    
    
    
    802
    
    
    
    39
    
    
    
    3,974Operating expensesResearch and development
    
    
    1,320
    
    
    
    1,704
    
    
    
    3,995
    
    
    
    6,395Manufacturing
    
    
    
    
    
    
    422
    
    
    
    
    
    
    
    3,148General and administrative
    
    
    1,377
    
    
    
    2,120
    
    
    
    4,873
    
    
    
    7,827Depreciation
    
    
    67
    
    
    
    111
    
    
    
    199
    
    
    
    3172,764
    
    
    
    4,357
    
    
    
    9,067
    
    
    
    17,687Loss from Operations
    
    
    (2,760
    )
    
    
    (3,555
    )
    
    
    (9,028
    )
    
    
    (13,713
    )Other (income) lossInvestment and other, net
    
    
    (16
    )
    
    
    14
    
    
    
    17
    
    
    
    (114
    )Change in fair value of warrant liability
    
    
    3,201
    
    
    
    
    
    
    
    5,703
    
    
    
    3,185
    
    
    
    14
    
    
    
    5,720
    
    
    
    (114
    )Net loss
    
    
    (5,945
    )
    
    
    (3,569
    )
    
    
    (14,748
    )
    
    
    (13,599
    )Other comprehensive income
    
    
    
    
    
    
    31
    
    
    
    
    
    
    
    Comprehensive loss
    
    $
    (5,945
    )
    
    $
    (3,538
    )
    
    $
    (14,748
    )
    
    $
    (13,599
    )Basic and diluted loss per share
    
    $
    (0.24
    )
    
    $
    (0.18
    )
    
    $
    (0.68
    )
    
    $
    (0.70
    )Weighted average number of common shares outstanding
    
    
    24,713,794
    
    
    
    19,492,432
    
    
    
    21,749,318
    
    
    
    19,490,011
  4




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ONCOTHYREON INC.
 
 Condensed Consolidated Statements of Stockholders Equity
(in thousands, except share amounts)
(Unaudited)
 AccumulatedAdditional
    
    
    
    
    
    
    OtherCommon Stock
    
    
    Paid-in
    
    
    Accumulated
    
    
    ComprehensiveShares
    
    
    Amount
    
    
    Capital
    
    
    Deficit
    
    
    LossBalance at January 1, 2008
    
    
    19,485,889
    
    
    $
    324,992
    
    
    $
    13,636
    
    
    $
    (321,543
    )
    
    $
    (5,066
    )Stock-based compensation expense
    
    
    
    
    
    
    
    
    
    
    1,509
    
    
    
    
    
    
    
    Net income
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    7,125
    
    
    
    Conversion of restricted share units
    
    
    6,543
    
    
    
    51
    
    
    
    (51
    )
    
    
    
    
    
    
    Balance at December 31, 2008
    
    
    19,492,432
    
    
    $
    325,043
    
    
    $
    15,094
    
    
    $
    (314,418
    )
    
    $
    (5,066
    )Stock-based compensation expense
    
    
    
    
    
    
    
    
    
    
    981
    
    
    
    
    
    
    
    Issuance of common stock
    
    
    6,159,553
    
    
    
    19,986
    
    
    
    
    
    
    
    
    
    
    
    Conversion of restricted share units
    
    
    9,920
    
    
    
    76
    
    
    
    (76
    )
    
    
    
    
    
    
    Net loss
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (14,748
    )
    
    
    Balance at September 30, 2009
    
    
    25,661,905
    
    
    $
    345,105
    
    
    $
    15,999
    
    
    $
    (329,166
    )
    
    $
    (5,066
    )
  5




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##### Table of Contents



ONCOTHYREON INC.
 
 Condensed Consolidated Statements of Cash Flows
(in thousands)
(Unaudited)
 Nine months ended September 30,2009
    
    
    2008OperatingNet loss
    
    $
    (14,748
    )
    
    $
    (13,599
    )Adjustments to reconcile net loss to net cash used in operating activitiesDepreciation
    
    
    199
    
    
    
    317Stock-based compensation expense
    
    
    981
    
    
    
    1,140Recognition of unearned revenue
    
    
    (12
    )
    
    
    (2,022
    )Proceeds from collaborative arrangements
    
    
    
    
    
    
    7,060Loss on disposal of plant and equipment
    
    
    5
    
    
    
    Change in fair value of warrant liability
    
    
    5,703
    
    
    
    Net change in non-cash working capital balances from operationsAccounts receivable
    
    
    1,801
    
    
    
    432Government grant receivable
    
    
    (116
    )
    
    
    398Prepaid expenses
    
    
    103
    
    
    
    57Inventory
    
    
    
    
    
    
    (5,159
    )Accounts payable and accrued liabilities
    
    
    (1,844
    )
    
    
    (466
    )Deposits
    
    
    
    
    
    
    (354
    )Net cash used in operating activities
    
    
    (7,928
    )
    
    
    (12,196
    )InvestingPurchase of short-term investments
    
    
    
    
    
    
    (22,376
    )Redemption of short-term investments
    
    
    
    
    
    
    34,248Collection of notes receivable
    
    
    
    
    
    
    (686
    )Purchase of plant and equipment
    
    
    (462
    )
    
    
    150Net cash provided (used) in investing activities
    
    
    (462
    )
    
    
    11,336FinancingProceeds on issuance of common stock and warrants, net
    
    
    24,204
    
    
    
    Repayment of capital lease obligations
    
    
    
    
    
    
    (78
    )Net cash provided (used) in financing activities
    
    
    24,204
    
    
    
    (78
    )15,814
    
    
    
    (938
    )Effect of exchange rate fluctuations on cash and cash equivalents
    
    
    
    
    
    
    281Increase (decrease) in cash and cash equivalents
    
    
    15,814
    
    
    
    (657
    )Cash and cash equivalents, beginning of period
    
    
    19,166
    
    
    
    12,035Cash and cash equivalents, end of period
    
    $
    34,980
    
    
    $
    11,378Supplemental disclosure of cash flow informationAmount of interest paid in the period
    
    $
    
    
    
    $
    6
  6




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ONCOTHYREON INC.
 Notes to the Condensed Consolidated Financial Statements
Three and nine months ended September 30, 2009 and 2008
(Unaudited)
 1. DESCRIPTION OF BUSINESS
   2. BASIS OF PRESENTATION
     3. RECENT ACCOUNTING PRONOUNCEMENTS
 Fair Value Measurements
 Fair
Value Measurements Effective Date of FASB Statement No. 157
  7




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Collaborative Arrangements
 Collaborative Arrangements
 Instruments Indexed to an Entitys Own Stock
 Determining
Whether an Instrument (or an Embedded Feature) is Indexed to an Entitys Own Stock Accounting for Derivative Instruments and Hedging
Activities Accounting for Derivative Financial Instruments Indexed to, and Potentially
Settled in, a Companys Own Stock
 4. FAIR VALUE MEASUREMENTS
  
    
    Level 1  quoted prices in active markets for identical assets or liabilities;
    
    Level 2  observable inputs other than Level 1 prices such as quoted prices for similar
assets or liabilities, quoted prices in markets that are not active, or other inputs that
are observable or can be corroborated by observable market data for substantially the full
term of the assets or liabilities; and
    
    Level 3  unobservable inputs that are supported by little or no market activity and
that are significant to the fair value of the assets or liabilities.
  Fair Value Measurements at September 30, 2009Significant other
    
    SignificantQuoted prices in
    
    observable
    
    unobservableTotal carrying
    
    active markets
    
    inputs
    
    inputsvalue
    
    (Level 1)
    
    (Level 2)
    
    (Level 3)Cash equivalents
    
    $
    32,039
    
    
    $
    32,039
    
    
    $
    
    
    
    $
    Warrant liability
    
    
    9,921
    
    
    
    
    
    
    
    
    
    
    
    9,921
 5. RESEARCH AND DEVELOPMENT
  8




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6. SHARE CAPITAL
 Stock Transactions
 (a) Loss Per Share
  Three months ended
    
    Nine months endedSeptember 30,
    
    September 30,2009
    
    2008
    
    2009
    
    2008Numerator:Net loss (in 000s)
    
    $
    5,945
    
    
    $
    3,569
    
    
    $
    14,748
    
    
    $
    13,599Denominator:Weighted average shares
outstanding used to compute earnings
per share  basic
    
    
    24,713,794
    
    
    
    19,492,432
    
    
    
    21,749,318
    
    
    
    19,490,011Effective of dilutive options and RSUs
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Weighted average shares outstanding
and dilutive securities used to
compute earnings per share  diluted
    
    
    24,713,794
    
    
    
    19,492,432
    
    
    
    21,749,318
    
    
    
    19,490,011
  (b) Registration Statement
  (c) Equity financing
   9




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##### Table of Contents



7. WARRANTS
 .
 Three and nine months endedSeptember 30,2009
    
    2008Exercise price
    
    $
    3.92
    
    
    $
    Market value of stock at end of period
    
    $
    5.21
    
    
    $
    Expected dividend rate
    
    
    N/A
    
    
    
    N/AExpected volatility
    
    
    74
    %
    
    
    N/ARisk-free interest rate
    
    
    2.2
    %
    
    
    N/AExpected life in years
    
    
    4.65
    
    
    
    N/AShares underlying warrants outstanding classified as liabilities
    
    
    2,909,244
    
    
    
    Shares underlying warrants outstanding classified as equity
    
    
    1,021,174
    
    
    
    795,150
   Initial measurement at May 26, 2009
    
    $
    4,218Revaluation of warrant liability at September 30, 2009
    
    
    5,703Balance at September 30, 2009
    
    $
    9,921
 8. STOCK-BASED COMPENSATION
 Stock Option Plan
    Three months ended
    
    Nine months endedSeptember 30,
    
    September 30,2009
    
    2008
    
    2009
    
    2008CDN$  Weighted average
grant-date fair value for stock
options granted in CDN$
    
    $
    
    
    
    $ 
    
    $
    
    
    
    $
    3.84US$  Weighted average
grant-date fair value for stock
options granted in US$
    
    $
    4.93
    
    
    $ 
    
    $
    1.38
    
    
    $
    2.93Expected dividend rate
    
    
    0
    %
    
    
    
    
    0
    %
    
    
    0
    %Expected volatility
    
    
    89.97
    %
    
    
    
    
    97.57
    %
    
    
    114.46
    %Risk-free interest rate
    
    
    2.84
    %
    
    
    
    
    2.34
    %
    
    
    3.09
    %Expected life of options in years
    
    
    6
    
    
    
    
    
    6
    
    
    
    6
 10




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##### Table of Contents



Restricted Share Unit Plan
    9. INVESTMENT AND OTHER, NET
  10. CONTINGENCIES, COMMITMENTS, AND GUARANTEES
 Royalties
   Guarantees
    11




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##### Table of Contents



11. FINANCIAL INSTRUMENTS
  Foreign Exchange Risk
  Accounts Receivable, Government Grant Receivable and Accounts Payable and Accrued Liabilities
  Notes Receivable
  Notes Payable and Class UA Preferred Stock
  Limitations
  
 Item 2. Managements Discussion and Analysis of Financial Condition and Results of Operations
 The information in this Item 2  Managements Discussion and Analysis of Financial Condition
and Results of Operations should be read in conjunction with our condensed consolidated financial
statements and related notes included in Part I, Item 1 of this quarterly report. This discussion
contains forward-looking statements based on current expectations that involve risks and
uncertainties, such as our plans, objectives, expectations and intentions. Any statements
contained in this discussion that are not statements of historical fact may be deemed to be
forward-looking statements. Words such as believes, anticipates, plans, expects, will,
intends, potential, possible and similar expressions are intended to identify forward-looking
statements. These forward-looking statements include, but are not limited to, the following: our
expectations regarding future expenses; clinical and pre-clinical development activities, including
our plans to substantially complete the pre-clinical development of BGLP40 in 2010, our goal to
initiate clinical development of BGLP40 in 2011 and our decision to initiate two or more Phase 2
trials for PX-866 in 2010; our expectations regarding receipt of a milestone payment from Merck KGaA in 2009;
our expectations regarding the timing and results of the Phase 3 trials for Stimuvax; our ability
to secure collaboration arrangements with pharmaceutical companies to complete the development and
commercialization of our product candidates, including PX-12; and the use and adequacy of cash
resources. Forward-looking statements involve risks and uncertainties related to our business and
the general economic environment, many beyond our control. These risks, uncertainties and other
factors could cause actual results to differ materially from those anticipated in the
forward-looking statements. Factors that might cause such a difference include, but are not limited
to, those discussed in this quarterly report in Part II, Item 1A  Risk Factors, and elsewhere
in this quarterly report You should not place
 12




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undue reliance on these forward-looking statements. These statements, like all statements in
this quarterly report, speak only as of their date, and we undertake no obligation to update or
revise these statements in light of future developments.
 Overview
         13




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Key Financial Metrics
 Revenue
  Contract Research and Development
 14




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Contract Manufacturing
 Licensing Revenue from Collaborative Agreements
 Expenses
 Research and Development/Manufacturing
     15




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##### Table of Contents



General and Administrative
 Depreciation
 Investment and other income
 Interest expense
 Change in fair value of warrant liability.
 Critical Accounting Policies and Significant Judgments and Estimates
    16




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Results of Operations for the Three and Nine Month Periods Ended September 30, 2009 and September 30, 2008
  Overview
 Three Months Ended
    
    
    
    
    
    Nine Months EndedSeptember 30,
    
    %
    
    September 30,
    
    %2009
    
    2008
    
    Change
    
    2009
    
    2008
    
    Change(In millions, except per
    
    
    
    
    
    (In millions, except pershare amounts)
    
    
    
    
    
    share amounts)Revenue
    
    $
    
    
    
    $
    0.8
    
    
    
    N/M
    +
    
    $
    
    
    
    $
    4.0
    
    
    
    N/M
    +Expenses
    
    
    2.7
    
    
    
    4.4
    
    
    
    (38.6
    )%
    
    
    9.1
    
    
    
    17.6
    
    
    
    (48.3
    )%Change in fair
value of warrant
liability
    
    
    3.2
    
    
    
    
    
    
    
    N/M
    +
    
    
    5.7
    
    
    
    
    
    
    
    N/M
    +Net loss
    
    $
    5.9
    
    
    $
    3.6
    
    
    
    63.9
    %
    
    $
    14.7
    
    
    $
    13.6
    
    
    
    8.1
    %Basic and diluted
loss per share
    
    $
    0.24
    
    
    $
    0.18
    
    
    
    33.3
    %
    
    $
    0.68
    
    
    $
    0.70
    
    
    
    (2.9
    )%
 
 +N/M
    
    Not meaningful  Revenue
 Three Months Ended
    
    
    
    
    
    
    Nine Months EndedSeptember 30,
    
    
    %
    
    
    September 30,
    
    
    %2009
    
    
    2008
    
    
    Change
    
    
    2009
    
    
    2008
    
    
    Change(In millions)
    
    
    
    
    
    
    (In millions)Contract manufacturing
    
    $
    
    
    
    $
    0.4
    
    
    
    N/M +
    
    
    $
    
    
    
    $
    2.9
    
    
    
    N/M +License revenue from
collaborative agreements
    
    
    
    
    
    
    0.4
    
    
    
    N/M +
    
    
    
    
    
    
    
    1.0
    
    
    
    N/M +$
    
    
    
    $
    0.8
    
    
    
    N/M +
    
    
    $
    
    
    
    $
    3.9
    
    
    
    N/M +
 
 +N/M
    
    Not meaningful   Research and Development / Manufacturing Expenses
 Three Months Ended
    
    
    
    
    
    
    Nine Months EndedSeptember 30,
    
    
    %
    
    
    September 30,
    
    
    %2009
    
    
    2008
    
    
    Change
    
    
    2009
    
    
    2008
    
    
    Change(In millions)
    
    
    
    
    
    
    
    
    
    
    (In millions)Research and development
    
    $
    1.3
    
    
    $
    1.7
    
    
    
    (23.5
    )%
    
    $
    4.0
    
    
    $
    6.4
    
    
    
    (37.5
    )%Manufacturing
    
    
    
    
    
    
    0.4
    
    
    
    N/M
    +
    
    
    
    
    
    
    3.1
    
    
    
    N/M
    +$
    1.3
    
    
    $
    2.1
    
    
    
    (38.1
    )%
    
    $
    4.0
    
    
    $
    9.5
    
    
    
    (57.9
    )%
 
 +N/M
    
    Not meaningful  17




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General and Administrative Expense
 Three Months Ended
    
    
    
    
    
    Nine Months EndedSeptember 30,
    
    %
    
    September 30,
    
    %2009
    
    2008
    
    Change
    
    2009
    
    2008
    
    Change(In millions)
    
    
    
    
    
    (In millions)General and administrative
    
    $
    1.4
    
    
    $
    2.1
    
    
    
    (33.3
    )%
    
    $
    4.9
    
    
    $
    7.8
    
    
    
    (37.2
    )%
   Change in Fair Value of Warrant Liability
 Three Months Ended
    
    
    
    
    
    Nine Months EndedSeptember 30,
    
    %
    
    September 30,
    
    %2009
    
    2008
    
    Change
    
    2009
    
    2008
    
    Change(In millions)
    
    
    
    
    
    (In millions)Change in fair
value of warrant
liability
    
    $
    3.2
    
    
    $
    
    
    
    
    N/M +
    
    
    $
    5.7
    
    
    $
    
    
    
    
    N/M +
 
 +N/M
    
    Not meaningful The $3.2 million and $5.7 million increase in change in fair value of warrant liability for
the three and nine month periods ended September 30, 2009, respectively, relative to the
comparable prior year periods was attributable to the warrants issued in connection with the May
26, 2009 financing. These warrants are classified as liabilities in accordance with the
Derivatives and Hedging Topic of the FASB ASC and accordingly, the fair market value of the
warrants is recorded on the balance sheet at issuance and marked to market at each financial
reporting period. The expense therefore, reflects the change in fair value of the warrants from
the date of issuance to the reporting period and is estimated using the Black-Scholes
option-pricing model.
 Liquidity and Capital Resources
 Cash, Cash Equivalents, and Working Capital
  18




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Cash Flows From Operating Activities
  Cash Flows From Investing Activities
  Contractual Obligations and Contingencies
  Payments Due by PeriodLess than
    
    
    
    
    
    
    
    
    
    More ThanTotal
    
    1 Year
    
    1-3 Years
    
    3-5 Years
    
    5  Years(In thousands)Operating leases  premises
    
    $
    5,267
    
    
    $
    503
    
    
    $
    1,016
    
    
    $
    1,169
    
    
    $
    2,579
  19




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Guarantees and Indemnification
  Off-Balance Sheet Arrangements
  Recent Accounting Pronouncements
    Determining
Whether an Instrument (or an Embedded Feature) is Indexed to an Entitys Own Stock Accounting for Derivative Instruments and Hedging
Activities
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Accounting for Derivative Financial Instruments
Indexed to, and Potentially Settled in, a Companys Own Stock
 21




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Item 3. Quantitative and Qualitative Disclosures About Market Risk
 Foreign Currency Exchange Risk
  Interest Rate Sensitivity
  
 Item 4. Controls and Procedures
 Evaluation of Disclosure Controls and Procedures
  Changes in Internal Control Over Financial Reporting
  Inherent Limitation on the Effectiveness of Internal Controls
  22




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##### Table of Contents



PART II  OTHER INFORMATION
 
 Item 1. Legal Proceedings
  
 Item 1A. Risk Factors
 Set forth below and elsewhere in this report, and in other documents we file with the SEC are
descriptions of risks and uncertainties that could cause actual results to differ materially from
the results contemplated by the forward-looking statements contained in this report. Because of the
following factors, as well as other variables affecting our operating results, past financial
performance should not be considered a reliable indicator of future performance and investors
should not use historical trends to anticipate results or trends in future periods. The risks and
uncertainties described below are not the only ones facing us. Other events that we do not
currently anticipate or that we currently deem immaterial also affect our results of operations and
financial condition.
 Risks Relating to our Business
 Our ability to continue with our planned operations is dependent on our success at raising
additional capital sufficient to meet our obligations on a timely basis. If we fail to obtain
additional financing when needed, we may be unable to complete the development, regulatory approval
and commercialization of our product candidates.
  
    
    our commercialization activities and arrangements;
 
    
    the progress of our research and development programs;
 
    
    the progress of our pre-clinical and clinical testing;
 
    
    the time and cost involved in obtaining regulatory approvals for our product
candidates;
 
    
    the cost of filing, prosecuting, defending and enforcing any patent claims and other
intellectual property rights with respect to our intellectual property;
 
    
    the effect of competing technological and market developments;
 
    
    the effect of changes and developments in our existing collaborative, licensing and
other relationships; and
 
    
    the terms of any new collaborative, licensing and other arrangements that we may
establish.
  Our near-term success is highly dependent on the success of our lead product candidate, Stimuvax,
and we cannot be certain that it will be successfully developed or receive regulatory approval or
be successfully commercialized.
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Stimuvax and our other vaccine product candidates are based on novel technologies, which may raise
new regulatory issues that could delay or make FDA approval more difficult.
   We have a history of net losses, we anticipate additional losses and we may never become
profitable.
  There is no assurance that we will be granted regulatory approval for any of our product
candidates.
  We are dependent upon our collaborative relationship with Merck KGaA to develop and commercialize
our lead product candidate, Stimuvax.
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We currently rely on third party manufacturers to supply our product candidates, which could delay
or prevent the clinical development and commercialization of our product candidates.
     Any failure or delay in commencing or completing clinical trials for our product candidates could
severely harm our business.
  
    
    our or our collaborators ability to obtain regulatory approval to commence a
clinical trial;
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##### Table of Contents




    
    our or our collaborators ability to manufacture or obtain from third parties
materials sufficient for use in pre-clinical studies and clinical trials;
 
    
    delays in patient enrollment and variability in the number and types of patients
available for clinical trials;
 
    
    poor effectiveness of product candidates during clinical trials;
 
    
    safety issues or side effects;
 
    
    governmental or regulatory delays and changes in regulatory requirements, policy and
guidelines; and
 
    
    varying interpretation of data by the FDA and similar foreign regulatory agencies.
  The failure to enroll patients for clinical trials may cause delays in developing our product
candidates.
    Even if regulatory approval is received for our product candidates, the later discovery of
previously unknown problems with a product, manufacturer or facility may result in restrictions,
including withdrawal of the product from the market.
  
    
    warning letters;
 
    
    fines;
 
    
    product recalls;
 
    
    withdrawal of regulatory approval;
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##### Table of Contents




    
    operating restrictions;
 
    
    disgorgement of profits;
 
    
    injunctions; and
 
    
    criminal prosecution.
  Failure to obtain regulatory approval in foreign jurisdictions would prevent us from marketing our
products internationally.
  Our product candidates may never achieve market acceptance even if we obtain regulatory approvals.
  
    
    our ability to provide acceptable evidence of safety and efficacy;
 
    
    the prevalence and severity of adverse side effects;
 
    
    availability, relative cost and relative efficacy of alternative and competing
treatments;
 
    
    the effectiveness of our marketing and distribution strategy;
 
    
    publicity concerning our products or competing products and treatments; and
 
    
    our ability to obtain sufficient third party insurance coverage or reimbursement.
  If we are unable to obtain, maintain and enforce our proprietary rights, we may not be able to
compete effectively or operate profitably.
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##### Table of Contents




    
    obtain patent and other proprietary protection for our technology, processes and
product candidates;
 
    
    defend patents once issued;
 
    
    preserve trade secrets; and
 
    
    operate without infringing the patents and proprietary rights of third parties.
   
    
    we might not have been the first to make the inventions covered by any of our
patents, if issued, or our pending patent applications;
 
    
    we might not have been the first to file patent applications for these inventions;
 
    
    others may independently develop similar or alternative technologies or products
and/or duplicate any of our technologies and/or products;
 
    
    it is possible that none of our pending patent applications will result in issued
patents or, if issued, these patents may not be sufficient to protect our technology or
provide us with a basis for commercially-viable products and may not provide us with any
competitive advantages;
 
    
    if our pending applications issue as patents, they may be challenged by third parties
as infringed, invalid or unenforceable under U.S. or foreign laws;
 
    
    if issued, the patents under which we hold rights may not be valid or enforceable; or
 
    
    we may develop additional proprietary technologies that are not patentable and which
may not be adequately protected through trade secrets, if for example a competitor were
to independently develop duplicative, similar or alternative technologies.
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If any products we develop become subject to unfavorable pricing regulations, third party
reimbursement practices or healthcare reform initiatives, our ability to successfully commercialize
our products will be impaired.
  29




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##### Table of Contents



Governments often impose strict price controls, which may adversely affect our future
profitability.
  We face potential product liability exposure, and if successful claims are brought against us, we
may incur substantial liability for a product candidate and may have to limit its
commercialization.
  
    
    decreased demand for our product candidates;
 
    
    impairment of our business reputation;
 
    
    withdrawal of clinical trial participants;
 
    
    costs of related litigation;
 
    
    substantial monetary awards to patients or other claimants;
 
    
    loss of revenues; and
 
    
    the inability to commercialize our product candidates.
  We face substantial competition, which may result in others discovering, developing or
commercializing products before, or more successfully, than we do.
  Stimuvax
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##### Table of Contents



Small Molecule Products
   
    
    design and develop products that are superior to other products in the market;
 
    
    attract qualified scientific, medical, sales and marketing and commercial personnel;
 
    
    obtain patent and/or other proprietary protection for our processes and product
candidates;
 
    
    obtain required regulatory approvals; and
 
    
    successfully collaborate with others in the design, development and commercialization
of new products.
  If we are unable to enter into collaborations with partners to perform sales and marketing
functions, or build these functions ourselves, we will not be able to commercialize our product
candidates.
  
    
    our inability to recruit and retain adequate numbers of effective sales and marketing
personnel;
 
    
    the inability of sales personnel to obtain access to or persuade adequate numbers of
physicians to prescribe our products;
 
    
    the lack of complementary products to be offered by sales personnel, which may put us
at a competitive disadvantage relative to companies with more extensive product lines;
and
 
    
    unforeseen costs and expenses associated with creating a sales and marketing
organization.
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If we lose key personnel, or we are unable to attract and retain highly-qualified personnel on a
cost-effective basis, it would be more difficult for us to manage our existing business operations
and to identify and pursue new growth opportunities.
   Our business is subject to increasingly complex environmental legislation that has increased both
our costs and the risk of noncompliance.
  If we fail to establish and maintain proper and effective internal controls, our ability to produce
accurate financial statements on a timely basis could be impaired, which would adversely affect our
consolidated operating results, our ability to operate our business, and our stock price.
    32




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If we are required to redeem the shares of our Class UA preferred stock, our financial condition
may be adversely affected.
     We may expand our business through the acquisition of companies or businesses or in-licensing
product candidates that could disrupt our business and harm our financial condition.
  
    
    substantial cash expenditures;
    
    potentially dilutive issuance of equity securities;
    
    incurrence of debt and contingent liabilities, some of which may be difficult or
impossible to identify at the time of acquisition;
    
    difficulties in assimilating the operations of the acquired companies;
    
    diverting our managements attention away from other business concerns;
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##### Table of Contents




    
    entering markets in which we have limited or no direct experience; and
    
    potential loss of our key employees or key employees of the acquired companies or
businesses.
  Risks Related to the Ownership of Our Common Stock
 Our common stock may become ineligible for listing on The NASDAQ Stock Market, which would
materially adversely affect the liquidity and price of our common stock.
    The trading price of our common stock may be volatile.
  
    
    the results of pre-clinical testing and clinical trials by us, our collaborators, our
competitors and/or companies that are developing products that are similar to ours
(regardless of whether such products are potentially competitive with ours);
    
    technological innovations or new therapeutic products;
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##### Table of Contents




    
    governmental regulations;
    
    developments in patent or other proprietary rights;
    
    litigation;
    
    public concern as to the safety of products developed by us or others;
    
    comments by securities analysts;
    
    the issuance of additional shares of common stock, or securities convertible into, or
exercisable or exchangeable for, shares of our common stock in connection with
financings, acquisitions or otherwise;
    
    the perception that shares of our common stock may be delisted from The NASDAQ Stock
Market;
    
    the incurrence of debt;
    
    general market conditions in our industry or in the economy as a whole; and
    
    political instability, natural disasters, war and/or events of terrorism.
  Because we do not expect to pay dividends on our common stock, stockholders will benefit from an
investment in our common stock only if it appreciates in value.
  We expect to raise additional capital in the future; however, such capital may not be available to
us on reasonable terms, if at all, when or as we require additional funding. If we issue
additional shares of our common stock or other securities that may be convertible into, or
exercisable or exchangeable for, our common stock, our existing stockholders would experience
further dilution.
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We can issue shares of preferred stock that may adversely affect the rights of a stockholder of our
common stock.
  
    
    adversely affect the voting power of the holders of our common stock;
    
    make it more difficult for a third party to gain control of us;
    
    discourage bids for our common stock at a premium;
    
    limit or eliminate any payments that the holders of our common stock could expect to
receive upon our liquidation; or
    
    otherwise adversely affect the market price or our common stock.
  We expect our quarterly operating results to fluctuate in future periods, which may cause our stock
price to fluctuate or decline.
  36




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Item 6. Exhibits
 ExhibitNumber
    
    Description10.1
    
    Form of Restricted Share Unit Agreement under the Companys Amended and Restated
Restricted Share Unit Plan (incorporated by reference from Exhibit 10.1 to Current
Report on Form 8-K filed on June 15, 2009).10.2
    
    Offer Letter dated June 9, 2009 between the Company and Scott Peterson, Ph.D.
(incorporated by reference from Exhibit 10.2 to Current Report on Form 8-K filed on
June 15, 2009).10.3
    
    Offer Letter dated July 6, 2009 between the Company and Diana Hausman, M.D.
(incorporated by reference from Exhibit 10.1 to Current Report on Form 8-K filed on
August 4, 2009).12.1
    
    Ratio of Earnings to Fixed Charges.31.1
    
    Certification of Robert L. Kirkman, M.D., President and Chief Executive Officer,
pursuant to Exchange Act Rules 13a-14(a) and 15d-14(a), as adopted pursuant to
Section 302 of the Sarbanes-Oxley Act of 2002.31.2
    
    Certification of Shashi K. Karan, Corporate Controller, pursuant to Exchange Act
Rules 13a-14(a) and 15d-14(a), as adopted pursuant to Section 302 of the
Sarbanes-Oxley Act of 2002.32.1
    
    Certification of Robert L. Kirkman, M.D., President and Chief Executive Officer,
pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the
Sarbanes-Oxley Act of 2002.32.2
    
    Certification of Shashi K. Karan, Corporate Controller, pursuant to 18 U.S.C.
Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
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SIGNATURES
  ONCOTHYREON INC.
(Registrant)Date: November 13, 2009
    /s/ Shashi K. KaranShashi K. Karan
Corporate Controller and Corporate Secretary 38




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##### Table of Contents



INDEX OF EXHIBITS
 ExhibitNumber
    
    Description10.1
    
    Form of Restricted Share Unit Agreement under the Companys Amended and Restated
Restricted Share Unit Plan (incorporated by reference from Exhibit 10.1 to Current
Report on Form 8-K filed on June 15, 2009).10.2
    
    Offer Letter dated June 9, 2009 between the Company and Scott Peterson, Ph.D.
(incorporated by reference from Exhibit 10.2 to Current Report on Form 8-K filed on
June 15, 2009).10.3
    
    Offer Letter dated July 6, 2009 between the Company and Diana Hausman, M.D.
(incorporated by reference from Exhibit 10.1 to Current Report on Form 8-K filed on
August 4, 2009).12.1
    
    Ratio of Earnings to Fixed Charges.31.1
    
    Certification of Robert L. Kirkman, M.D., President and Chief Executive Officer,
pursuant to Exchange Act Rules 13a-14(a) and 15d-14(a), as adopted pursuant to
Section 302 of the Sarbanes-Oxley Act of 2002.31.2
    
    Certification of Shashi K. Karan, Corporate Controller, pursuant to Exchange Act
Rules 13a-14(a) and 15d-14(a), as adopted pursuant to Section 302 of the
Sarbanes-Oxley Act of 2002.32.1
    
    Certification of Robert L. Kirkman, M.D., President and Chief Executive Officer,
pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the
Sarbanes-Oxley Act of 2002.32.2
    
    Certification of Shashi K. Karan, Corporate Controller, pursuant to 18 U.S.C.
Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
 39