##### 



UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 FORM 10-Q
 þ
    
    QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the quarterly period ended March 31, 2008
 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: 001-33452
 TomoTherapy Incorporated
  Wisconsin
    
    39-1914727(State or other jurisdiction of incorporation or organization)
    
    (I.R.S. Employer Identification No.)1240 Deming Way, Madison, Wisconsin
    
    53717(Address of principal executive offices)
    
    (Zip Code)
 (608) 824-2800
 þ o
  Large accelerated filer o
    
    Accelerated filer o
    
    Non-accelerated filer þ
    
    Smaller reporting company o(Do not check if a smaller reporting company)
 o þ




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##### 



TomoTherapy Incorporated
Index
 PagePart I  FINANCIAL INFORMATIONItem 1. Financial Statements (unaudited)
    
    
    3Condensed Consolidated Balance Sheets
    
    
    3Condensed Consolidated Statements of Operations
    
    
    4Condensed Consolidated Statements of Cash Flows
    
    
    5Notes to the Condensed Consolidated Financial Statements
    
    
    6Item 2. Managements Discussion and Analysis of Financial Condition and Results of Operations
    
    
    15Item 3. Quantitative and Qualitative Disclosures about Market Risk
    
    
    21Item 4. Controls and Procedures
    
    
    21Part II  OTHER INFORMATIONItem 1. Legal Proceedings
    
    
    23Item 1A. Risk Factors
    
    
    23Item 2. Unregistered Sales of Equity Securities and Use of Proceeds
    
    
    25Item 3. Defaults Upon Senior Securities
    
    
    26Item 4. Submission of Matters to a Vote of Security Holders
    
    
    26Item 5. Other Information
    
    
    26Item 6. Exhibits
    
    
    27SIGNATURES
    
    
    28INDEX TO EXHIBITS
  2




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##### 



PART I. FINANCIAL INFORMATION
 
 Item 1. Financial Statements
 TOMOTHERAPY INCORPORATED AND SUBSIDIARIES
 
 CONDENSED
CONSOLIDATED BALANCE SHEETS
(In thousands, except share amounts)
(unaudited)
 March 31,
    
    
    December 31,2008
    
    
    2007ASSETSCash and cash equivalents
    
    $
    165,827
    
    
    $
    191,780Accounts receivable
    
    
    37,543
    
    
    
    44,596Inventories
    
    
    68,558
    
    
    
    53,171Deferred tax assets
    
    
    6,832
    
    
    
    3,433Prepaid expenses and other current assets
    
    
    2,615
    
    
    
    1,622Total current assets
    
    
    281,375
    
    
    
    294,602Property and equipment, net
    
    
    21,218
    
    
    
    19,894Deferred tax assets
    
    
    6,082
    
    
    
    6,027Other non-current assets, net
    
    
    7,523
    
    
    
    6,642TOTAL ASSETS
    
    $
    316,198
    
    
    $
    327,165LIABILITIES AND SHAREHOLDERS EQUITYAccounts payable
    
    $
    16,593
    
    
    $
    17,655Accrued expenses
    
    
    14,493
    
    
    
    21,699Accrued warranty
    
    
    7,268
    
    
    
    7,973Deferred revenue
    
    
    16,088
    
    
    
    15,517Customer deposits
    
    
    20,731
    
    
    
    20,309Total current liabilities
    
    
    75,173
    
    
    
    83,153Other non-current liabilities
    
    
    5,366
    
    
    
    5,318Total liabilities
    
    
    80,539
    
    
    
    88,471SHAREHOLDERS EQUITYPreferred stock, $1 par value, 10,000,000 shares authorized at
March 31, 2008 and December 31, 2007; zero shares
issued and outstanding at March 31, 2008 and
December 31, 2007, respectively
    
    
    
    
    
    
    Common stock, $.01 par value, 200,000,000 shares
authorized at March 31, 2008 and December 31, 2007;
50,116,680 and 49,740,577 shares issued and
outstanding at March 31, 2008 and December 31, 2007, respectively
    
    
    501
    
    
    
    497Additional paid-in capital
    
    
    653,699
    
    
    
    651,725Treasury stock, 1,632 shares at cost
    
    
    
    
    
    
    Accumulated other comprehensive income (loss)
    
    
    636
    
    
    
    (523
    )Accumulated deficit
    
    
    (419,177
    )
    
    
    (413,005
    )Total shareholders equity
    
    
    235,659
    
    
    
    238,694TOTAL LIABILITIES AND SHAREHOLDERS EQUITY
    
    $
    316,198
    
    
    $
    327,165
  3




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##### 



TOMOTHERAPY INCORPORATED AND SUBSIDIARIES
 
 CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
(In thousands, except per share amounts)
(unaudited)
 Three months ended March 31,2008
    
    
    2007Revenue
    
    $
    38,900
    
    
    $
    51,163Cost of revenue
    
    
    30,682
    
    
    
    29,352Gross profit
    
    
    8,218
    
    
    
    21,811Operating expenses:Research and development
    
    
    9,525
    
    
    
    7,155Selling, general and administrative
    
    
    10,668
    
    
    
    8,625Total operating expenses
    
    
    20,193
    
    
    
    15,780Income (loss) from operations
    
    
    (11,975
    )
    
    
    6,031Other income (expense):Interest income
    
    
    1,774
    
    
    
    132Interest expense
    
    
    (11
    )
    
    
    (38
    )Other income (expense), net
    
    
    (74
    )
    
    
    7Total other income
    
    
    1,689
    
    
    
    101Income (loss) before income tax
    
    
    (10,286
    )
    
    
    6,132Income tax expense (benefit)
    
    
    (4,114
    )
    
    
    2,246Net income (loss)
    
    
    (6,172
    )
    
    
    3,886Accretion of redeemable convertible preferred stock
    
    
    
    
    
    
    (134,948
    )Net loss attributable to common shareholders
    
    $
    (6,172
    )
    
    $
    (131,062
    )Net loss per share attributable to common shareholdersBasic and diluted
    
    $
    (0.12
    )
    
    $
    (12.13
    )Weighted average common shares outstanding used in computing net loss per
share attributable to common shareholdersBasic and diluted
    
    
    50,024
    
    
    
    10,804
  4




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##### 



TOMOTHERAPY INCORPORATED AND SUBSIDIARIES
 
 CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
(In thousands)
(unaudited)
 Three months ended March 31,2008
    
    
    2007Cash flows from operating activities:Net income (loss)
    
    $
    (6,172
    )
    
    $
    3,886Adjustments to reconcile net income (loss) to net cash used in operating activities:Depreciation and amortization
    
    
    1,958
    
    
    
    1,471Noncash charge for stock compensation
    
    
    1,009
    
    
    
    810Deferred income tax provision (benefit)
    
    
    (3,454
    )
    
    
    1,792Deferred rent
    
    
    66
    
    
    
    107Loss on disposal of property and equipment
    
    
    
    
    
    
    4Change in carrying value of convertible preferred stock warrants
    
    
    
    
    
    
    58Provision for warranties
    
    
    1,925
    
    
    
    2,625Provision for obsolete inventory
    
    
    75
    
    
    
    891Changes in operating assets and liabilities:Accounts receivable
    
    
    12,558
    
    
    
    (20,364
    )Inventories
    
    
    (14,412
    )
    
    
    (12,790
    )Prepaid expenses and other current assets
    
    
    (977
    )
    
    
    (898
    )Accounts payable
    
    
    (7,465
    )
    
    
    3,951Accrued expenses
    
    
    (7,344
    )
    
    
    (2,136
    )Accrued warranty
    
    
    (2,630
    )
    
    
    (1,921
    )Deferred revenue
    
    
    301
    
    
    
    8,571Customer deposits
    
    
    422
    
    
    
    (3,484
    )Other non-current liabilities
    
    
    67
    
    
    
    Net cash used in operating activities
    
    
    (24,073
    )
    
    
    (17,427
    )Cash flows from investing activities:Purchase of property and equipment
    
    
    (2,425
    )
    
    
    (1,929
    )Purchase of test systems
    
    
    (1,531
    )
    
    
    (66
    )Capitalization of software costs
    
    
    (36
    )
    
    
    Payments for intangible assets
    
    
    
    
    
    
    (5
    )Net cash used in investing activities
    
    
    (3,992
    )
    
    
    (2,000
    )Cash flows from financing activities:Payments on notes payable
    
    
    (16
    )
    
    
    (8
    )Proceeds from exercise of warrants
    
    
    7
    
    
    
    523Proceeds from exercise of stock options
    
    
    962
    
    
    
    1,455Net cash provided by financing activities
    
    
    953
    
    
    
    1,970Effect of exchange rate changes on cash
    
    
    1,159
    
    
    
    (36
    )Decrease in cash and cash equivalents
    
    
    (25,953
    )
    
    
    (17,493
    )Cash and cash equivalents at beginning of period
    
    
    191,780
    
    
    
    20,137Cash and cash equivalents at end of period
    
    $
    165,827
    
    
    $
    2,644
  5




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##### 



NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
(Unaudited)
 NOTE A  DESCRIPTION OF BUSINESS
  NOTE B  SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES
 Principles of Consolidation
  Basis of Presentation
    Use of Estimates
  Inventories
  6




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##### 



March 31,
    
    
    December 31,2008
    
    
    2007Raw materials
    
    $
    45,852
    
    
    $
    41,405Work-in-process
    
    
    10,578
    
    
    
    8,722Finished goods
    
    
    12,128
    
    
    
    3,044$
    68,558
    
    
    $
    53,171
 Accrued Expenses
  March 31,
    
    
    December 31,2008
    
    
    2007Commissions and payroll-related
    
    $
    4,921
    
    
    $
    6,597Bonuses
    
    
    956
    
    
    
    5,249Other
    
    
    8,616
    
    
    
    9,853$
    14,493
    
    
    $
    21,699
 Warranty Cost
  March 31,
    
    
    March 31,2008
    
    
    2007Balance, beginning of period
    
    $
    7,973
    
    
    $
    5,307Charged to cost of revenue
    
    
    1,925
    
    
    
    2,625Adjustments related to change in estimate
    
    
    345
    
    
    
    175Actual product warranty expenditures
    
    
    (2,975
    )
    
    
    (2,096
    )Balance, end of period
    
    $
    7,268
    
    
    $
    6,011
 Revenue Recognition
     7




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##### 



Software Revenue Recognition Software Revenue Recognition with Respect to Certain Agreements.
 Stock-Based Compensation
 Share-Based
Payment
  Three months ended March 31,2008
    
    
    2007Cost of revenue
    
    $
    149
    
    
    $
    115Research and development
    
    
    255
    
    
    
    182Selling, general and administrative
    
    
    440
    
    
    
    513Income tax benefit
    
    
    (142
    )
    
    
    (131
    )$
    702
    
    
    $
    679
 Net Income (Loss) Per Share of Common Stock
  8




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##### 



Three months ended March 31,2008
    
    
    2007Net income (loss) per common share:Basic and diluted:Net income (loss)
    
    $
    (0.12
    )
    
    $
    0.36Net loss attributable to common shareholders
    
    $
    (0.12
    )
    
    $
    (12.13
    )Weighted average common shares outstanding used in:Basic and diluted
    
    
    50,024
    
    
    
    10,804
   Three months ended March 31,2008
    
    
    2007Preferred stock (as if converted)
    
    
    
    
    
    
    25,677Contingent common shares
    
    
    
    
    
    
    1,289Stock options and warrants
    
    
    5,985
    
    
    
    7,2405,985
    
    
    
    34,206
  9




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##### 



Three months ended March 31,2008
    
    
    2007HistoricalNumerator:Net loss attributable to common shareholders
    
    $
    (6,172
    )
    
    $
    (131,062
    )Denominator:Weighted-average shares of common stock outstanding
    
    
    50,024
    
    
    
    10,804Net loss attributable to common shareholders per share  basic and
diluted
    
    $
    (0.12
    )
    
    $
    (12.13
    )Pro forma (unaudited)Numerator:Net loss
    
    
    
    
    
    $
    (131,062
    )Pro forma adjustment to add back preferred stock accretion
    
    
    
    
    
    
    134,948Pro forma net income available for shareholders
    
    
    
    
    
    $
    3,886Denominator for pro forma basic net income per share:Weighted-average shares of common stock outstanding
    
    
    
    
    
    
    10,804Pro forma adjustments to reflect assumed conversion of preferred
stock (as if converted)
    
    
    
    
    
    
    25,498Pro forma adjustment to reflect assumed conversion of contingent
common shares (as if converted)
    
    
    
    
    
    
    1,289Shares used to compute pro forma basic net income per common
share
    
    
    
    
    
    
    37,591Pro forma basic net income per share
    
    
    
    
    
    $
    0.10Denominator for pro forma diluted net income per share:Weighted-average shares of common stock outstanding
    
    
    
    
    
    
    10,804Pro forma adjustments to reflect assumed conversion of preferred
stock (as if converted)
    
    
    
    
    
    
    25,498Pro forma adjustment to reflect assumed conversion of contingent
common shares (as if converted)
    
    
    
    
    
    
    1,289Pro forma adjustments to reflect assumed exercise of warrants and
stock options using treasury stock method
    
    
    
    
    
    
    4,577Shares used to compute pro forma diluted net income per share
    
    
    
    
    
    
    42,168Pro forma diluted net income per share
    
    
    
    
    
    $
    0.09
 Segment Information
 Disclosures About Segments of an Enterprise and Related Information,
  Three months ended March 31,2008
    
    
    2007Product
    
    $
    32,487
    
    
    $
    48,466Service and other
    
    
    6,413
    
    
    
    2,697$
    38,900
    
    
    $
    51,163
 Recent Accounting Pronouncements
 , Accounting for Uncertainty in Income Taxes  an
Interpretation of FASB Statement No. 109
 10




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##### 



Accounting for Income Taxes
 Fair Value Measurements
 The Fair Value Option for Financial Assets and
Financial Liabilities
 Business Combinations Accounting and Reporting of Noncontrolling Interest in Consolidated Financial
Statements, an amendment of ARB No. 51
 Disclosures about Derivative Instruments and
Hedging Activities, an amendment of FASB Statement No. 133
 NOTE C  INCOME TAXES
    11




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##### 



NOTE D  COMMITMENTS AND CONTINGENCIES
   NOTE E  TEMPORARY EQUITY AND SHAREHOLDERS EQUITY (DEFICIT)
 Redeemable Convertible Preferred Stock
  Warrants
  Issuers Accounting under
FASB Statement No. 150 for Freestanding Warrants and Other Similar Instruments on Shares That Are
Redeemable
 12




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##### 



Contingent Common Shares
 Application of Issue No 98-5 to Certain Convertible Instruments .
 NOTE F  STOCK OPTIONS
   Options OutstandingWeighted-AverageShares
    
    
    
    
    
    
    Weighted-
    
    
    Remaining
    
    
    AggregateAvailable
    
    
    Number of
    
    
    Average Exercise
    
    
    Contractual
    
    
    instrinsicfor Grant
    
    
    Shares
    
    
    Price
    
    
    Term (in years)
    
    
    valueBalance at December 31, 2007
    
    
    2,077
    
    
    
    6,331
    
    
    $
    4.24Granted
    
    
    (49
    )
    
    
    49
    
    
    
    17.04Exercised
    
    
    
    
    
    
    (372
    )
    
    
    2.58Cancelled
    
    
    4
    
    
    
    (26
    )
    
    
    6.92Balance at March 31, 2008
    
    
    2,032
    
    
    
    5,982
    
    
    $
    5.11
    
    
    
    5.19
    
    
    $
    56,814Exercisable at March 31, 2008
    
    
    
    
    
    
    2,079
    
    
    $
    3.03
    
    
    
    5.68
    
    
    $
    23,579
  13




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##### 



Three months ended March 31,2008
    
    2007Employee Stock Option PlansExpected term (in years)
    
    
    4.25
    
    
    
    N/ARisk-free interest rate
    
    
    2.7
    %
    
    
    N/AExpected volatility
    
    
    46
    %
    
    
    N/AExpected dividend
    
    
    
    
    
    
    N/AExpected forfeiture rate
    
    
    5.4
    %
    
    
    N/A
 NOTE G  RELATED PARTY TRANSACTIONS
  NOTE H OTHER EVENTS
   14




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##### 



Item 2. Managements Discussion and Analysis of Financial Condition and Results of Operations
 The following discussion and analysis of our financial condition and results of operations
should be read together with our unaudited condensed consolidated financial statements and related
notes included elsewhere in this Form 10-Q . It should also be read in conjunction with our audited
consolidated financial statements and related notes included in our Annual Report on Form 10-K for
the year ended December 31, 2007. This discussion and analysis contains forward-looking statements
that involve risks, uncertainties and assumptions. Our actual results may differ materially from
those anticipated in these forward-looking statements as a result of many factors, including but
not limited to those set forth under Risk Factors and elsewhere in this report. We urge you not
to place undue reliance on these forward-looking statements, which speak only as of the date of
this report. All forward-looking statements included in this report are based on information
available to us on the date of this report, and we assume no obligation to update any
forward-looking statements contained in this report.
 Forward-looking Statements
  Overview
   Financial Performance
  Revenue
  
    
    The Hi Art system has a lengthy sales cycle. We generally recognize revenue from a
system sale upon customer acceptance, and each installation represents a significant
component of our revenue for a particular period. While the majority of our orders in
backlog are delivered within twelve months, it occasionally takes longer until a system
has been
 15




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##### 



installed and accepted by the customer. Therefore, if a few customers defer installation
of the Hi Art system for even a short time, recognition of a significant amount of revenue
may be deferred to a subsequent period.
 
    
    We have not yet been negatively impacted by the current global economic conditions or
the tightening of the credit market. However, since the Hi Art system is a major
capital equipment purchase and may require funding through a credit facility or lease
arrangement, customers who have placed orders may have difficulty making payments or
customers who are in the process of placing orders may have difficulty obtaining credit.
Therefore, order cancellations could occur. In addition, potential new customers may
delay placing capital equipment orders in such situations, or may choose to purchase
equipment that is less costly.
    
    Our mix of customers may impact our average selling prices. Increased sales of the
Hi Art system outside of North America have tended to impact our gross margins favorably
due to higher average selling prices in these markets. We intend to continue to expand
our international selling efforts although we cannot be certain that favorable pricing
trends will continue.
    
    Our focus on sales to for-profit multi-center customers may require us to lower the
selling price of the Hi Art system, as these customers tend to be more price conscious
and may be motivated by quantity discounts. In addition, these orders may remain in
backlog longer than we have historically experienced.
    
    Our ability to demonstrate the clinical benefits of the Hi Art system compared to
competing systems is likely to be a factor in our ability to maintain the selling price
of the Hi Art system. To compete favorably with our competitors, we may need to perform
expensive clinical trials in order to prove the clinical benefit of the system or offer
additional features that could take a high level of time and expense to develop.
 Backlog.
 Customer concentration.
 Geographic breakdown
 Three months Ended March 31,2008
    
    2007North America
    
    
    77
    %
    
    
    50
    %Europe
    
    
    12
    %
    
    
    44
    %Asia-Pacific
    
    
    11
    %
    
    
    6
    %100
    %
    
    
    100
    %
 Cost of revenue
  Component supply and cost.
 16




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##### 



Service and support expenses.
  Operating expenses
  Nonoperating expenses
  Income tax expenses
 Multiple taxing jurisdictions.
 Income tax expense reserves.
 Research and development income tax credit.
 17




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##### 



Results of Operations
  Three months Ended March 31,2008
    
    
    2007Revenue
    
    
    100.0
    %
    
    
    100.0
    %Cost of revenue
    
    
    78.9
    %
    
    
    57.4
    %Gross profit
    
    
    21.1
    %
    
    
    42.6
    %Operating expenses:Research and development
    
    
    24.5
    %
    
    
    13.9
    %Selling, general and administrative
    
    
    27.4
    %
    
    
    16.9
    %Total operating expenses
    
    
    51.9
    %
    
    
    30.8
    %Income (loss) from operations
    
    
    -30.8
    %
    
    
    11.8
    %Other income (expense):Interest income
    
    
    4.6
    %
    
    
    0.3
    %Interest expense
    
    
    0.0
    %
    
    
    -0.1
    %Other income (expense), net
    
    
    -0.2
    %
    
    
    0.0
    %Total other income
    
    
    4.4
    %
    
    
    0.2
    %Income (loss) before income tax
    
    
    -26.4
    %
    
    
    12.0
    %Income tax expense (benefit)
    
    
    -10.6
    %
    
    
    4.4
    %Net income (loss)
    
    
    -15.8
    %
    
    
    7.6
    %
 Three Months Ended March 31, 2008 Compared to Three Months Ended March 31, 2007
 Revenue
   Cost of revenue
   18




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##### 



Research and development expenses
  Selling, general and administrative expenses
  Stock-based compensation
  Other income (expense)
  Income tax expense (benefit)
  Liquidity and Capital Resources
  Cash Flows
 Cash flows from operating activities
  19




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##### 



Cash flows from investing activities
   Cash flows from financing activities
    Financial Condition
  Loans and Available Borrowings
  Contractual Obligations and Commitments
  20




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##### 



Operating Capital and Capital Expenditure Requirements
  
    
    revenue generated by sales of the Hi Art system and service contracts;
    
    costs associated with our sales and marketing initiatives and manufacturing activities;
    
    the level of investment needed in our service and support infrastructure;
    
    costs of our research and development activities; and
    
    effects of competing technological and market developments.
  Off-Balance Sheet Arrangements
  Critical Accounting Policies and Estimates
   
 Item 3. Quantitative and Qualitative Disclosures about Market Risk
  
 Item 4. Controls and Procedures
  21




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##### 



22




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##### 



Part II. OTHER INFORMATION
 
 Item 1. Legal Proceedings
  
 Item 1A. Risk Factors
  Since substantially all of our revenue is derived from sales of the Hi Art system, and because of
the long sales cycle and high unit price of the Hi Art system, results will very significantly from
period to period and it may be difficult to compare our results of operations to prior periods.
  Our ability to maintain revenue growth and increase our profitability depends in part on
maintaining our average selling prices and increasing our gross margins, which we may not be able
to achieve.
  We face competition from numerous competitors, many of whom have greater resources than we do,
which may make it more difficult for us to achieve significant market penetration.
  23




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##### 



We may be delayed or prevented from implementing our long-term sales strategy if we fail to educate
clinicians and patients about the benefits of the Hi Art system and to implement enhancements to
the system in a timely manner.
   Our sales may be impacted, or we may be faced with order cancellations, if economic conditions in
the United States or elsewhere worsen and credit becomes more difficult to obtain on reasonable
terms.
  We rely on local distributors to market and distribute the Hi Art system in key markets.
  24




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##### 



Our reliance on single-source suppliers for critical components of the Hi Art system could harm our
ability to meet demand for our products in a timely and cost effective manner.
   Our success will depend on our ability to attract and retain qualified personnel as well as
effective management of our growth.
  We recently invested in continued development of a new compact proton therapy system through a
separate entity. If this development project is unsuccessful, or we are unable to raise the
additional capital that may be necessary for this project on acceptable terms, our ability to
diversify our business could be impaired.
  
 Item 2. Unregistered Sales of Equity Securities and Use of Proceeds
 (a) Sales of Unregistered Securities
  (b) Use of Proceeds from Public Offering of Common Stock
  25




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(c) Purchases of Equity Securities by the Issuer and Affiliated Purchasers
  
 Item 3. Defaults Upon Senior Securities
  
 Item 4. Submission of Matters to a Vote of Security Holders
  
 Item 5. Other Information
  26




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Item 6. Exhibits
 Exhibit Number
    
    Description2.1
    
    Equity Interest Transfer Agreement, dated April 17, 2008.(1)*10.1
    
    Stock Purchase Agreement dated as of April 25, 2008 by and among Compact Particle Acceleration
Corporation, TomoTherapy Incorporated and the other shareholders named therein.(2)10.2
    
    Shareholder Agreement dated as of April 25, 2008 by and among Compact Particle Acceleration
Corporation, TomoTherapy Incorporated and the other shareholders named therein.(2)10.3
    
    Investors Rights Agreement for Compact Particle Acceleration Corporation dated as of April 25,
2008 by and among Compact Particle Acceleration Corporation, TomoTherapy Incorporated and the other
shareholders named therein.(2)10.4
    
    Limited Exclusive License Agreement for Dielectric Wall Accelerator Technology for Particle and
Radiotherapy dated as of February 23, 2007 between The Regents of the University of California and
TomoTherapy Incorporated.(2)*10.5
    
    Amendment One dated as of April 8, 2008 to Limited Exclusive Patent License Agreement for
Dielectric Wall Accelerator Technology for Particle and Radiotherapy between Lawrence Livermore
National Security, LLC and TomoTherapy Incorporated.(2)*10.6
    
    Limited Exclusive Sublicense Agreement dated as of April 25, 2008 for Dielectric Wall Accelerator
Technology between TomoTherapy Incorporated and Compact Particle Acceleration Corporation.(2)*31.1
    
    Certification of Chief Executive Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.(3)31.2
    
    Certification of Chief Financial Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.(3)32.1
    
    Certification of Chief Executive Officer Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.(3)32.2
    
    Certification of Chief Financial Officer Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.(3)
 
 (1)
    
    Previously filed as an exhibit to Form 8-K/A on April 21, 2008.(2)
    
    Previously filed as an exhibit to Form 8-K on April 28, 2008.(3)
    
    Filed as an exhibit to this Form 10-Q.*
    
    Confidential treatment has been requested for portions of this exhibit. These portions have
been omitted from the Form 8-K and submitted separately to the Securities and Exchange
Commission. 27




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SIGNATURES
   TOMOTHERAPY INCORPORATED/s/ Frederick A. RobertsonFrederick A. RobertsonChief Executive OfficerTOMOTHERAPY INCORPORATED/s/ Stephen C. HathawayStephen C. HathawayChief Financial Officer and Treasurer 28