##### Table of Contents



UNITED STATES SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 Form 10-K/A
 (Amendment No. 1)
 þ
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF
THE SECURITIES EXCHANGE ACT OF 1934
 For the fiscal year ended December 31, 2010
 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
 (Exact name of Registrant as specified in its charter)
 Wisconsin(State or Other Jurisdiction of Incorporation or Organization)
    
    39-1914727(I.R.S. Employer Identification No.)1240 Deming Way, Madison, Wisconsin(Address of principal executive offices)
    
    53717(Zip Code)
 (608) 824-2800
 (Registrants telephone number, including area code)
 Securities registered pursuant to Section 12(b) of the Act:
 Title of Each Class
    
    Name of Each Exchange on Which RegisteredCommon Stock
    
    NASDAQ Global Select Market
 Securities registered pursuant to section 12(g) of the Act:
None
 o þ
 o þ
 þ o
 o o
 o
  Large accelerated filer o
Accelerated filer þ
Non-accelerated filer o(Do not check if a smaller reporting company)
Smaller reporting company o
 o þ




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EXPLANATORY NOTE




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##### 



TomoTherapy Incorporated
 INDEX
 PART IIIItem 10. Directors, Executive Officers and Corporate Governance
    
    
    1Item 11. Executive Compensation
    
    
    4Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Shareholder Matters
    
    
    17Item 13. Certain Relationships and Related Transactions, and Director Independence
    
    
    19Item 14. Principal Accountant Fees and Services
    
    
    20PART IVItem 15. Exhibits and Financial Statement Schedules
    
    
    22Signatures
    
    
    26Exhibit Index
    
    
    27EX-31.1EX-31.2EX-32.1EX-32.2




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##### Table of Contents



PART III
 
 Item 10. Directors, Executive Officers and Corporate Governance
 Executive Officers of the Registrant
  Name
    
    Age
    
    PositionFrederick A. Robertson
    
    
    55
    
    
    Chief Executive Officer, President and DirectorThomas E. Powell
    
    
    49
    
    
    Chief Financial Officer and TreasurerThomas Rockwell Mackie
    
    
    56
    
    
    Chairman of the Board of Directors and Co-FounderBrenda S. Furlow
    
    
    52
    
    
    Vice President, General Counsel and Corporate SecretaryEric A. Schloesser
    
    
    38
    
    
    Vice President, Operations and Business DevelopmentRafael L. Vaello
    
    
    47
    
    
    Chief Commercial Officer
 Frederick A. Robertson, M.D.
 Thomas E. Powell
 Thomas Rockwell Mackie, Ph.D.
 Brenda S. Furlow, J.D.,
 Eric A. Schloesser
 1




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##### Table of Contents



Rafael L. Vaello
 Directors of the Registrant
  Name
    
    Age
    
    Initial Year of Service as DirectorLance C. Balk
    
    
    53
    
    
    
    2010Sam R. Leno
    
    
    65
    
    
    
    2006Thomas Rockwell Mackie
    
    
    56
    
    
    
    1997H. Jonathan McCloskey
    
    
    42
    
    
    
    2009John J. McDonough
    
    
    74
    
    
    
    2004Cary J. Nolan
    
    
    68
    
    
    
    2001Carlos A. Perez
    
    
    76
    
    
    
    2005Frederick A. Robertson
    
    
    55
    
    
    
    2005Roy T. Tanaka
    
    
    63
    
    
    
    2008Frances S. Taylor
    
    
    64
    
    
    
    2006
 Lance C. Balk
 Sam R. Leno
 Thomas Rockwell Mackie, Ph.D.
 H. Jonathan McCloskey
 2




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##### Table of Contents



John J. McDonough
 Cary J. Nolan
 Carlos A. Perez, M.D.
 Frederick A. Robertson, M.D.
 Roy T. Tanaka
 Frances S. Taylor
 Committees of the Board of Directors
  3




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Audit Committee
  Compensation Committee
  Nominating and Governance Committee
  Nomination of Directors
  Section 16(a) Beneficial Ownership Reporting Compliance
  Code of Ethics
 http://www.tomotherapy.com
     
 Item 11. Executive Compensation
 Compensation Discussion and Analysis
  4




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The Role of the Compensation Committee
  Compensation Philosophy
  
    
    to attract, motivate and retain highly experienced executives who are vital to our
short- and long-term success, profitability and growth; and
    
    to create alignment with executives and shareholders by rewarding executives for the
achievement of strategic goals that successfully drive our performance, and thereby
enhance shareholder value.
 Determining Executive Compensation
  th th th
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    Intuitive Surgical IncAmerican Medical Systems
    
    Invacare CorpAnalogic Corp
    
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    Kinetic Concepts IncArthrocare Corp
    
    Masimo CorpC.R. Bard Inc
    
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    Meridian Bioscience IncCardiac Science Corp
    
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    Orthofix International NvCynosure Inc
    
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    Quidel CorpEdwards Lifesciences Corp
    
    Resmed IncEv3 Inc
    
    Sirona Dental Systems IncExactech Inc
    
    Sonosite IncGen-Probe Inc
    
    Steris CorpGreatbatch Inc
    
    Symmetry Medical IncHaemonetics Corp
    
    Thoratec CorpHealthtronics Inc
    
    Varian Medical Systems IncHill-Rom Holdings Inc
    
    Volcano CorpHologic Inc
    
    West Pharmaceutical Services IncHome Diagnostics Inc
    
    Wright Medical Group IncIcu Medical Inc
    
    Zoll Medical CorpIdexx Labs Inc
 5




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Elements of Compensation
  Base Salaries
 th th
 2010 Summary Compensation Table
 Annual Incentives
   6




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Payout Below
    
    Payout at
    
    
    
    
    
    Payout atMetric
    
    Weight
    
    Threshold
    
    Threshold
    
    Payout at Target
    
    MaximumCash Flow
    
    
    25
    %
    
    
    0
    %
    
    
    50
    %
    
    
    100
    %
    
    
    150
    %Operating Income
    
    
    25
    %
    
    
    0
    %
    
    
    50
    %
    
    
    100
    %
    
    
    150
    %Revenue Growth
    
    
    25
    %
    
    
    0
    %
    
    
    50
    %
    
    
    100
    %
    
    
    150
    %Average Service
Cost (ASC)
    
    
    25
    %
    
    
    0
    %
    
    
    50
    %
    
    
    100
    %
    
    
    150
    %
 Equity Incentives
   th
 7




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##### Table of Contents



2010 Grants of Plan-Based Awards
 Stock Ownership Guidelines
  Perquisites and Other Benefits
  Change in Control and Post Termination Compensation
 Employment Agreements  Severance and Change of Control Provisions.
 Tax Consequences of Incentive Plans
  Assessment of Risk
  8




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##### Table of Contents



Compensation Committee Report
   Frances S. Taylor (Chair)
Cary J. Nolan
Roy T. Tanaka
 9




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##### Table of Contents



2010 Summary Compensation Table
  Non-Equity
    
    
    
    
    
    Stock
    
    Option
    
    All OtherSalary
    
    Incentive
    
    Bonus
    
    Awards
    
    Awards
    
    Compensation
    
    TotalName and Principal Position
    
    Year
    
    ($)
    
    Compensation
    
    ($)
    
    ($) (1)
    
    ($) (1)
    
    ($) (2)
    
    ($)Frederick A. Robertson
    
    
    2010
    
    
    
    462,600
    
    
    
    623,123
    (6)
    
    
    
    
    
    
    1,030,250
    
    
    
    
    
    
    
    14,922
    
    
    
    2,130,895Chief Executive Officer &
    
    
    2009
    
    
    
    450,000
    
    
    
    
    
    
    
    138,024
    (7)
    
    
    850,950
    
    
    
    
    
    
    
    13,979
    
    
    
    1,452,953President
    
    
    2008
    
    
    
    443,750
    
    
    
    
    
    
    
    
    
    
    
    1,118,130
    
    
    
    
    
    
    
    13,529
    
    
    
    1,575,409Thomas E. Powell
    
    
    2010
    
    
    
    343,375
    
    
    
    231,264
    (6)
    
    
    
    
    
    
    447,287
    
    
    
    
    
    
    
    60,676
    (8)
    
    
    1,082,602Chief Financial Officer &
    
    
    2009
    
    
    
    176,519
    (3)
    
    
    
    
    
    
    88,260
    (10)
    
    
    731,000
    
    
    
    122,880
    
    
    
    38,688
    (9)
    
    
    1,157,347TreasurerRafael L. Vaello
    
    
    2010
    
    
    
    272,000
    
    
    
    183,193
    (6)
    
    
    
    
    
    
    357,893
    
    
    
    
    
    
    
    26,045
    
    
    
    839,131Chief Commercial Officer
    
    
    2009
    
    
    
    250,000
    
    
    
    
    
    
    
    44,091
    (7)
    
    
    465,000
    
    
    
    
    
    
    
    17,151
    
    
    
    776,2422008
    
    
    
    20,833
    (3)
    
    
    
    
    
    
    
    
    
    
    96,900
    
    
    
    
    
    
    
    
    
    
    
    117,733Eric A. Schloesser
    
    
    2010
    
    
    
    249,960
    
    
    
    168,349
    (6)
    
    
    
    
    
    
    297,980
    
    
    
    
    
    
    
    10,687
    
    
    
    726,976Vice President, Operations &
    
    
    2009
    
    
    
    240,000
    
    
    
    
    
    
    
    41,407
    (7)
    
    
    372,000
    
    
    
    
    
    
    
    9,863
    
    
    
    663,270Business Development
    
    
    2008
    
    
    
    172,183
    (4)
    
    
    
    
    
    
    
    
    
    
    203,130
    
    
    
    
    
    
    
    7,829
    
    
    
    383,142Brenda S. Furlow
    
    
    2010
    
    
    
    282,960
    
    
    
    190,574
    (6)
    
    
    
    
    
    
    357,893
    
    
    
    2,109
    
    
    
    15,650
    
    
    
    849,186Vice President, General
    
    
    2009
    
    
    
    241,125
    
    
    
    
    
    
    
    46,224
    (7)
    
    
    302,250
    
    
    
    1,563
    
    
    
    13,114
    
    
    
    604,276Counsel & Corporate Secretary
    
    
    2008
    
    
    
    165,500
    (5)
    
    
    
    
    
    
    
    
    
    
    164,959
    
    
    
    8,398
    
    
    
    10,850
    
    
    
    349,707
 
 (1)
    
    Aggregate fair value on date of grant computed in accordance with FASB ASC Topic 718. The
assumptions used in these calculations are discussed in Footnote J to the Companys financial
statements included in its Annual Report on Form 10-K for the year ended December 31, 2010.(2)
    
    This includes the contributions made on each named executive officers behalf to a 401(k)
plan, life and disability insurance premiums and in the case of Mr. Vaello, auto allowance.(3)
    
    Mr. Powell joined the Company on June 22, 2009 and Mr. Vaello joined the Company on December
1, 2008.(4)
    
    Mr. Schloesser took a leave of absence from June to September 2008.(5)
    
    Ms. Furlow assumed the role of Vice President, General Counsel and Corporate Secretary during
August 2008.(6)
    
    Bonus for 2010 paid in March 2011 in accordance with incentive plan terms.(7)
    
    Discretionary bonus related to 2009 performance period, paid in March 2010.(8)
    
    Mr. Powell received a relocation living allowance payment of $52,500 in addition to the
amounts mentioned in (2) above(9)
    
    Mr. Powell received a relocation living allowance payment of $34,500 in addition to the
amounts mentioned in (2) above.(10)
    
    Guaranteed bonus related to 2009 performance period, paid in March 2010. Employment Agreements
  Compensation and Other Benefits
  10




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##### Table of Contents



Named Executive Officers
    
    Base Salary(1)Frederick A. Robertson
    
    $
    475,200Thomas E. Powell
    
    
    351,750Rafael L. Vaello
    
    
    294,000Eric A. Schloesser
    
    
    260,000Brenda S. Furlow
    
    
    296,000
 
 (1)
    
    Base salaries were effective July 1, 2010. Severance and Change of Control Provisions
 Termination for Cause
 
 Termination by Executive for Good Reason
  Change of Control
  Termination Upon Death or Disability
  11




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Termination Upon Resignation or Retirement
  Definition of Separation from Service and Termination of Employment
  COBRA Group Health Insurance
  Payment of Accrued Obligations
  Timing of Severance Payment
  Tax Adjustments
  Severance and Change of Control Payments
   12




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##### Table of Contents



TotalSalary
    
    Bonus
    
    COBRA
    
    Other
    
    SeveranceName
    
    ($) (1)
    
    ($)
    
    ($) (2)
    
    ($) (3)
    
    ($)Thomas E. Powell
    
    
    351,750
    
    
    
    88,260
    
    
    
    17,150
    
    
    
    10,000
    
    
    
    467,160Rafael L. Vaello
    
    
    294,000
    
    
    
    22,046
    
    
    
    17,150
    
    
    
    10,000
    
    
    
    343,196Eric A. Schloesser
    
    
    260,000
    
    
    
    20,704
    
    
    
    13,099
    
    
    
    10,000
    
    
    
    303,803Brenda S. Furlow
    
    
    296,000
    
    
    
    23,112
    
    
    
    1,460
    
    
    
    10,000
    
    
    
    330,572
 
 (1)
    
    Equals 12 months of base salary paid in lump sum.(2)
    
    Plan provides 12 months of continuation benefits at the current level. No increase in
healthcare premiums is factored into these amounts. This benefit ceases when the executive
becomes eligible for other employer-sponsored healthcare.(3)
    
    Other consists of executive outplacement services up to a maximum of $10,000.  TotalSalary
    
    Bonus
    
    COBRA
    
    Other
    
    SeveranceName
    
    ($) (1)
    
    ($) (2)
    
    ($) (3)
    
    ($) (4)
    
    ($)Thomas E. Powell
    
    
    703,500
    
    
    
    351,750
    
    
    
    34,301
    
    
    
    10,000
    
    
    
    1,099,551Rafael L. Vaello
    
    
    588,000
    
    
    
    294,000
    
    
    
    34,301
    
    
    
    10,000
    
    
    
    926,301Eric A. Schloesser
    
    
    520,000
    
    
    
    260,000
    
    
    
    26,198
    
    
    
    10,000
    
    
    
    816,198Brenda S. Furlow
    
    
    592,000
    
    
    
    296,000
    
    
    
    2,920
    
    
    
    10,000
    
    
    
    900,920
 
 (1)
    
    Equals 24 months of base salary.(2)
    
    Equals two times the greater of average (i) actual annual bonus paid over past two years or
(ii) target bonus.(3)
    
    Plan provides 24 months of continuation benefits at the executives current participation
level. No increase in healthcare premiums is factored into these amounts. This benefit
ceases when the executive becomes eligible for other employer sponsored healthcare.(4)
    
    Other consists of executive outplacement services up to a maximum of $10,000. 13




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Other Employment-Related Agreements
  2010 Grants of Plan-Based Awards
  AllOtherStockAwards;
    
    GrantNumber
    
    Date Fairof
    
    Value ofEstimated Future Payouts Under
    
    Shares
    
    Stock andNon-Equity Incentive Plan
    
    of Stock
    
    OptionGrant
    
    Awards (1)
    
    or Units
    
    AwardsName
    
    Date
    
    Threshold ($)
    
    Target ($)
    
    Maximum ($)
    
    (#)
    
    ($)Frederick A.
RobertsonShort-Term
Incentives
    
    
    
    
    
    
    237,600
    
    
    
    475,200
    
    
    
    712,800Long-Term
Incentives
    
    
    8/24/2010
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    325,000
    
    
    
    1,030,250Thomas E. PowellShort-Term
Incentives
    
    
    
    
    
    
    87,938
    
    
    
    175,875
    
    
    
    263,813Long-Term
Incentives
    
    
    8/24/2010
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    141,100
    
    
    
    447,287Rafael L. VaelloShort-Term
Incentives
    
    
    
    
    
    
    73,500
    
    
    
    147,000
    
    
    
    220,500Long-Term
Incentives
    
    
    8/24/2010
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    112,900
    
    
    
    357,893Eric A. SchloesserShort-Term
Incentives
    
    
    
    
    
    
    65,000
    
    
    
    130,000
    
    
    
    195,000Long-Term
Incentives
    
    
    8/24/2010
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    94,000
    
    
    
    297,980Brenda S. FurlowShort-Term
Incentives
    
    
    
    
    
    
    74,000
    
    
    
    148,000
    
    
    
    222,000Long-Term
Incentives
    
    
    8/24/2010
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    112,900
    
    
    
    357,893
 
 (1)
    
    The non-equity incentive plan award amounts are pursuant to the Companys annual incentive
plan as discussed previously. 14




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Compensation Discussion and Analysis
 Elements of Compensation  Annual Incentives. Compensation
Discussion and Analysis  Elements of Compensation  Equity Incentives.
 2010 Outstanding Equity Awards at Fiscal Year End
  Option Awards (1)


    
    Stock Awards (2)MarketNumber
    
    Value ofNumber of
    
    
    
    
    
    
    
    
    
    of Shares
    
    Shares orNumber of
    
    Securities
    
    
    
    
    
    
    
    
    
    or Units
    
    Units ofSecurities
    
    Underlying
    
    
    
    
    
    
    
    
    
    of Stock
    
    StockUnderlying
    
    Unexercised
    
    Option
    
    
    
    
    
    That have
    
    ThatOption
    
    Unexercised
    
    Options
    
    Exercise
    
    Option
    
    Not
    
    Have NotGrant
    
    Options
    
    Unexercisable
    
    Price
    
    Expiration
    
    Vested
    
    VestedName
    
    Date
    
    Exercisable (#)
    
    (#)
    
    ($)
    
    Date
    
    (#)
    
    ($)Frederick A.
Robertson
    
    
    1/3/2005
    
    
    
    846,218
    
    
    
    
    
    
    
    2.8199
    
    
    
    1/3/201511/17/2005
    
    
    
    204,000
    
    
    
    
    
    
    
    3.4559
    
    
    
    11/17/201112/7/2006
    
    
    
    136,000
    
    
    
    
    
    
    
    6.7500
    
    
    
    12/7/20128/28/2008
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    61,100
    
    
    
    220,5719/29/2009
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    122,000
    
    
    
    440,4208/24/2010
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    325,000
    
    
    
    1,173,250Thomas E. Powell
    
    
    6/22/2009
    
    
    
    25,000
    
    
    
    75,000
    
    
    
    2.6600
    
    
    
    6/22/20156/22/2009
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    75,000
    
    
    
    270,7509/29/2009
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    66,666
    
    
    
    240,6648/24/2010
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    141,100
    
    
    
    509,371Rafael L. Vaello
    
    
    12/10/2008
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    15,000
    
    
    
    54,1509/29/2009
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    66,666
    
    
    
    240,6648/24/2010
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    112,900
    
    
    
    407,569Eric A. Schloesser
    
    
    11/17/2005
    
    
    
    68,000
    
    
    
    
    
    
    
    3.4559
    
    
    
    11/17/201112/7/2006
    
    
    
    108,800
    
    
    
    
    
    
    
    6.7500
    
    
    
    12/7/20128/28/2008
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    11,100
    
    
    
    40,0719/29/2009
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    53,333
    
    
    
    192,5328/24/2010
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    94,000
    
    
    
    339,340Brenda S. Furlow
    
    
    5/9/2007
    
    
    
    7,500
    
    
    
    2,500
    
    
    
    19.0000
    
    
    
    5/9/20138/28/2008
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    6,667
    
    
    
    24,06812/10/2008
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    4,433
    
    
    
    16,0039/29/2009
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    43,333
    
    
    
    156,4328/24/2010
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    112,900
    
    
    
    407,569
 
 (1)
    
    Options vest 25% each year beginning one year after the date of grant, except for the options
granted on December 7, 2006, which vest 50% on December 7, 2008 and 25% each year thereafter.(2)
    
    Restricted stock awards vest one-third each year beginning one year after the date of grant,
except for the award granted to Mr. Vaello on December 10, 2008 and the award granted to Mr.
Powell on June 22, 2009, which vest 25% per year over four years. 15




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##### Table of Contents



2010 Option Exercises and Shares Vested
 Stock AwardsNumber ofSharesAcquired on
    
    Value RealizedVesting
    
    on VestingName
    
    (#)
    
    ($)Frederick A. Robertson
    
    
    122,100
    
    
    
    423,680Thomas E. Powell
    
    
    58,334
    
    
    
    186,752Rafael L. Vaello
    
    
    40,834
    
    
    
    144,252Eric A. Schloesser
    
    
    37,767
    
    
    
    132,141Brenda S. Furlow
    
    
    32,766
    
    
    
    114,881
 Director Compensation
  Board of Directors:Annual retainer per director
    
    $
    25,000Fee per meeting for a full board meeting
    
    $
    2,000Audit Committee:Annual retainer for chairperson
    
    $
    15,000Annual retainer for other members
    
    $
    10,000Fee per meeting
    
    $
    0Compensation Committee:Annual retainer for chairperson
    
    $
    10,000Annual retainer for other members
    
    $
    5,000Fee per meeting
    
    $
    0Nominating and Governance Committee:Annual retainer for chairperson
    
    $
    10,000Annual retainer for other members
    
    $
    5,000Fee per meeting
    
    $
    0
     16




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##### Table of Contents



FeesEarnedor Paid
    
    Stockin Cash
    
    Awards
    
    TotalName
    
    ($)
    
    ($)(1)
    
    ($)Lance C. Balk (2)
    
    
    28,945
    
    
    
    109,440
    (3)
    
    
    138,385Sam R. Leno
    
    
    45,000
    
    
    
    99,855
    (4)
    
    
    144,855H. Jonathan McCloskey
    
    
    45,000
    
    
    
    99,855
    (5)
    
    
    144,855John J. McDonough
    
    
    50,000
    
    
    
    99,855
    (4)
    
    
    149,855Carey J. Nolan
    
    
    50,000
    
    
    
    99,855
    (4)
    
    
    149,855Carlos A. Perez, M.D.
    
    
    40,000
    
    
    
    99,855
    (4)
    
    
    139,855Roy T. Tanaka
    
    
    41,250
    
    
    
    99,855
    (6)
    
    
    141,105Frances S. Taylor
    
    
    50,000
    
    
    
    99,855
    (4)
    
    
    149,855
 
 (1)
    
    Aggregate fair value on date of grant computed in accordance with FASB ASC Topic 718. The
assumptions used in these calculations are discussed in Footnote J to the Companys financial
statements included in its Annual Report on Form 10-K for the year ended December 31, 2010.(2)
    
    Mr. Balk joined the Board on May 5, 2010.(3)
    
    As of December 31, 2010, Mr. Balk had 24,750 shares of restricted stock outstanding.(4)
    
    As of December 31, 2010, Messrs. Leno, McDonough, Nolan and Perez, and Ms. Taylor each had
52,166 shares of restricted stock outstanding.(5)
    
    As of December 31, 2010, Mr. McCloskey had 29,756 unexercisable options and 31,500 shares of
restricted stock outstanding.(6)
    
    As of December 31, 2010, Mr. Tanaka had 9,568 unexercisable options and 46,166 shares of
restricted stock outstanding. Compensation Committee Interlocks and Insider Participation
  
 Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder
Matters
 Security Ownership of Certain Beneficial Owners and Management
  17




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##### Table of Contents



Number of
    
    PercentageShares
    
    of SharesBeneficially
    
    BeneficiallyOwned
    
    OwnedDirectors and executive officers:Frederick A. Robertson (1)
    
    
    2,291,423
    
    
    
    4.0
    %Thomas E. Powell (2)
    
    
    363,645
    
    
    
    *Rafael L. Vaello (3)
    
    
    230,115
    
    
    
    *Eric A. Schloesser (4)
    
    
    393,486
    
    
    
    *Brenda S. Furlow (5)
    
    
    214,787
    
    
    
    *T. Rockwell Mackie (6)
    
    
    1,822,446
    
    
    
    3.2
    %Lance C. Balk(7)
    
    
    52,900
    
    
    
    *Sam R. Leno (8)
    
    
    125,900
    
    
    
    *H. Jonathan McCloskey (9)
    
    
    94,493
    
    
    
    *John J. McDonough (10)
    
    
    160,997
    
    
    
    *Cary J. Nolan (11)
    
    
    197,183
    
    
    
    *Carlos A. Perez (12)
    
    
    125,900
    
    
    
    *Roy T. Tanaka (13 )
    
    
    100,244
    
    
    
    *Frances S. Taylor (14)
    
    
    119,900
    
    
    
    *All directors and executive officers as a group
    
    
    6,293,419
    
    
    
    10.8
    %
 
 *
    
    Less than one percent(1)
    
    Consists of 597,105 shares of common stock, 508,100 shares of restricted stock and 1,186,218
shares of common stock issuable upon the exercise of options exercisable within 60 days of the
date of this table.(2)
    
    Consists of 55,879 shares of common stock, 282,766 shares of restricted stock and 25,000
shares of common stock issuable upon the exercise of options exercisable within 60 days of the
date of this table.(3)
    
    Consists of 35,549 shares of common stock and 194,566 shares of restricted stock.(4)
    
    Consists of 58,253 shares of common stock, 158,433 shares of restricted stock and 176,800
shares of common stock issuable upon the exercise of options exercisable within 60 days of the
date of this table.(5)
    
    Consists of 37,454 shares of common stock, 167,333 shares of restricted stock and 10,000
shares of common stock issuable upon the exercise of options exercisable within 60 days of the
date of this table.(6)
    
    Consists of 1,687,250 shares of common stock, 57,066 shares of restricted stock and 78,130
shares of common stock issuable upon the exercise of options exercisable within 60 days of the
date of this table.(7)
    
    Consists of 30,400 shares of common stock and 22,500 shares of restricted stock.(8)
    
    Consists of 16,334 shares of common stock, 55,166 shares of restricted stock and 54,400
shares of common stock issuable upon the exercise of options exercisable within 60 days of the
date of this table.(9)
    
    Consists of 31,500 shares of restricted stock and 62,993 shares of common stock issuable upon
the exercise of options exercisable within 60 days of the date of this table.(10)
    
    Consists of 39,931 shares of common stock, 52,166 shares of restricted stock and 68,900
shares of common stock issuable upon the exercise of options exercisable within 60 days of the
date of this table.(11)
    
    Consists of 130,517 shares of common stock, 52,166 shares of restricted stock and 14,500
shares of common stock issuable upon the exercise of options exercisable within 60 days of the
date of this table.(12)
    
    Consists of 19,334 shares of common stock, 52,166 shares of restricted stock and 54,400
shares of common stock issuable upon the exercise of options exercisable within 60 days of the
date of this table. 18




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##### Table of Contents



(13)
    
    Consists of 7,334 shares of common stock, 46,166 shares of restricted stock and 46,744 shares
of common stock issuable upon the exercise of options exercisable within 60 days of the date
of this table.(14)
    
    Consists of 23,334 shares of common stock, 52,166 shares of restricted stock and 44,400
shares of common stock issuable upon the exercise of options exercisable within 60 days of the
date of this table. Changes in Control
    Securities Authorized for Issuance under Equity Compensation Plans
  Number of SecuritiesRemaining Available forFuture Issuance underNumber of Securities
    
    
    
    
    
    
    Equity Compensationto be Issued Upon
    
    
    Weighted-Average
    
    
    Plans (ExcludingExercise of
    
    
    Exercise Price of
    
    
    Securities Reflected inOutstanding Options
    
    
    Outstanding Options
    
    
    the First Column)Equity compensation plans
approved by security holders
    
    $
    4,315,088
    
    
    $
    5.04
    
    
    $
    2,157,646Equity compensation plans not
approved by security holders
    
    
    
    
    
    
    
    
    
    
    $
    4,315,088
    
    
    $
    5.04
    
    
    $
    2,157,646
 
 Item 13. Certain Relationships and Related Transactions, and Director Independence
 Review, Approval or Ratification of Related Person Transactions
  
    
    approved by a majority of the disinterested members of the Board of Directors; and
    
    on terms no less favorable to the Company than those that it believes could be obtained
from unaffiliated third parties.
  19




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##### Table of Contents



Transactions with Related Persons
  Director Independence
  
 Item 14. Principal Accountant Fees and Services
 Principal Accountant Fees and Services
  2010
    
    
    2009Audit fees
    
    $
    459,505
    
    
    $
    502,369Audit-related fees
    
    
    
    
    
    
    Tax fees
    
    
    136,516
    
    
    
    153,221All other fees
    
    
    84,729
    
    
    
    103,417Total
    
    $
    680,750
    
    
    $
    759,007
 Audit Fees
 Audit-Related Fees
 Tax Fees
 All Other Fees
 Policy on Audit Committee Pre-Approval of Audit and Permissible Non-Audit Services of Independent
Registered Public Accounting Firm
  20




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21




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##### Table of Contents



PART IV
 
 Item 15. Exhibits and Financial Statement Schedules
 1. Financial Statements
  2. Financial Statement Schedules
  3. Exhibits
 EXHIBIT INDEX
 ExhibitNumber
    
    Description2.1
    
    Agreement and Plan of Merger, dated as of March 6, 2011, among Parent, Merger Sub and the Company
 Incorporated by referenced to Exhibit 2.1 to the Companys current report of Form 8-K filed
with the SEC on March 7, 2011, File No. 001-33452.3.1
    
    Amended and Restated Articles of Incorporation of the Company  Incorporated herein by reference
to Exhibit 3.1 to the Companys quarterly report on Form 10-Q filed with the SEC on November 7,
2008, File No. 001-33452.3.2
    
    Amended and Restated Bylaws of the Company  Incorporated herein by reference to Exhibit 3.2 to
the Companys quarterly report on Form 10-Q filed with the SEC on November 7, 2008, File No.
001-33452.4.1
    
    Form of the Companys Common Stock Certificate  Incorporated herein by reference to Exhibit 4.1
to Amendment No. 2 to the Companys registration statement on Form S-1 filed with the SEC on
April 16, 2007, File No. 333-140600.10.1
    
    Lease Agreement, dated January 26, 2005, between the Company and Old Sauk Trails Park Limited
Partnership  Incorporated herein by reference to Exhibit 10.13 to the Companys registration
statement on Form S-1 filed with the SEC on February 12, 2007, File No. 333-140600.10.2
    
    Lease Agreement, dated October 28, 2005, between the Company and Adelphia, LLC  Incorporated
herein by reference to Exhibit 10.14 to the Companys registration statement on Form S-1 filed
with the SEC on February 12, 2007, File No. 333-140600.10.3+
    
    Incentive Stock Option Plan, as amended, and forms of option agreements thereunder 
Incorporated herein by reference to Exhibit 10.16 to the Companys registration statement on Form
S-1 filed with the SEC on February 12, 2007, File No. 333-140600.10.4+
    
    2000 Stock Option Plan, as amended, and forms of option agreements thereunder  Incorporated
herein by reference to Exhibit 10.17 to the Companys registration statement on Form S-1 filed
with the SEC on February 12, 2007, File No. 333-140600.10.5+
    
    2002 Stock Option Plan, as amended, and forms of option agreements thereunder  Incorporated
herein by reference to Exhibit 10.18 to the Companys registration statement on Form S-1 filed
with the SEC on February 12, 2007, File No. 333-140600.10.6
    
    Standard Terms and Conditions of Sale  Incorporated herein by reference to Exhibit 10.19 to the
Companys registration statement on Form S-1 filed with the SEC on February 12, 2007, File No.
333-140600.10.7
    
    International Standard Terms and Conditions of Sale  Incorporated herein by reference to
Exhibit 10.20 to the Companys registration statement on Form S-1 filed with the SEC on February
12, 2007, File No. 333-140600.10.8
    
    Tomo Lifecycle Care and Partnership Terms and Conditions  Incorporated herein by reference to
Exhibit 10.21 to the Companys registration statement on Form S-1 filed with the SEC on February
12, 2007, File No. 333-140600.10.9
    
    Development and OEM Supply Agreement, dated January 27, 2003, between the Company and Analogic
Corporation  Incorporated herein by reference to Exhibit 10.11 to Amendment No. 2 to the
Companys registration statement on Form S-1 filed with the SEC on April 16, 2007, File No.
333-140600.10.10+
    
    2007 Equity Incentive Plan  Incorporated herein by reference to Exhibit 10.19 to Amendment No.
2 to the
 22




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##### Table of Contents



ExhibitNumber
    
    DescriptionCompanys registration statement on Form S-1 filed with the SEC on April 16, 2007, File
No. 333-140600.10.11+
    
    First Amendment to 2007 Equity Incentive Plan, dated May 1, 2009  Incorporated herein by
reference to Exhibit 99.1 to the Companys current report on Form 8-K filed with the SEC on May
5, 2009, File No. 001-33452.10.12+
    
    Second Amendment to 2007 Equity Incentive Plan, dated December 9, 2010  Incorporated herein by
reference to Exhibit 10.12 to the Companys annual report on Form 10-K filed with the SEC on
March 3, 2011, File No. 001-33452.10.13+
    
    2007 Employee Stock Purchase Plan, as amended  Incorporated herein by reference to Exhibit
10.20 to Amendment No. 2 to the Companys registration statement on Form S-1 filed with the SEC
on April 16, 2007, File No. 333-140600.10.14
    
    Form of Noncompetition Agreement  Incorporated herein by reference to Exhibit 10.27 to
Amendment No. 2 to the Companys registration statement on Form S-1 filed with the SEC on April
16, 2007, File No. 333-140600.10.15
    
    Form of Assignment of Inventions Agreement  Incorporated herein by reference to Exhibit 10.28
to Amendment No. 2 to the Companys registration statement on Form S-1 filed with the SEC on
April 16, 2007, File No. 333-140600.10.16
    
    Form of Confidentiality Agreement  Incorporated herein by reference to Exhibit 10.29 to
Amendment No. 2 to the Companys registration statement on Form S-1 filed with the SEC on April
16, 2007, File No. 333-140600.10.17
    
    License Agreement 98-0228, dated February 22, 1999, between the Company and Wisconsin Alumni
Research Foundation  Incorporated herein by reference to Exhibit 10.4 to Amendment No. 3 to the
Companys registration statement on Form S-1 filed with the SEC on April 19, 2007, File No.
333-140600.10.18
    
    Amendment to License Agreement 98-0228, dated April 16, 2007, between the Company and Wisconsin
Alumni Research Foundation  Incorporated herein by reference to Exhibit 10.31 to the Companys
registration statement on Form S-1 filed with the SEC on September 21, 2007, File No. 333-146219.10.19
    
    Amendment to License Agreement 98-0228, dated December 16, 2008, between the Company and
Wisconsin Alumni Research Foundation  Incorporated herein by reference to Exhibit 10.2 to the
Companys current report on Form 8-K filed with the SEC on December 30, 2008, File No. 001-33452.10.20
    
    Stock Purchase Agreement, dated April 25, 2008, between Compact Particle Acceleration Corporation
and its investors  Incorporated herein by reference to Exhibit 10.1 to the Companys current
report on Form 8-K filed with the SEC on April 28, 2008, File No. 001-33452.10.21
    
    Shareholder Agreement, dated April 25, 2008, between Compact Particle Acceleration Corporation
and its investors  Incorporated herein by reference to Exhibit 10.2 to the Companys current
report on Form 8-K filed with the SEC on April 28, 2008, File No. 001-33452.10.22
    
    Investors Rights Agreement, dated April 25, 2008, between Compact Particle Acceleration
Corporation and its investors  Incorporated herein by reference to Exhibit 10.3 to the
Companys current report on Form 8-K filed with the SEC on April 28, 2008, File No. 001-33452.10.23
    
    Limited Exclusive License Agreement, dated February 23, 2007, between the Company and Regents of
the University of California  Incorporated herein by reference to Exhibit 10.4 to the Companys
current report on Form 8-K filed with the SEC on April 28, 2008, File No. 001-33452.10.24
    
    Amendment One to Limited Exclusive License Agreement, dated April 8, 2008, between the Company
and Lawrence Livermore National Security, LLC  Incorporated herein by reference to Exhibit 10.5
to the Companys current report on Form 8-K filed with the SEC on April 28, 2008, File No.
001-33452.10.25
    
    Limited Exclusive Sublicense Agreement, dated April 25, 2008, between the Company and Compact
Particle Acceleration Corporation  Incorporated herein by reference to Exhibit 10.6 to the
Companys current report on Form 8-K filed with the SEC on April 28, 2008, File No. 001-33452.10.26
    
    Supply Agreement, dated June 25, 2008, between the Company and Hitachi Medical Corporation 
Incorporated herein by reference to Exhibit 10.1 to the Companys current report on Form 8-K
filed with the SEC on June 30, 2008, File No. 001-33452.10.27
    
    Form of Indemnification Agreement for Directors, Executive Officers, and Controller 
Incorporated herein by reference to Exhibit 10.3 to the Companys quarterly report on Form 10-Q
filed with the SEC on November 7, 2008, File No. 001-33452.10.28+
    
    Form of Employment Agreement, dated November 5, 2008, between the Company and Brenda S. Furlow
and Rafael L. Vaello  Incorporated herein by reference to Exhibit 10.37 to the Companys annual
report on Form
 23




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##### Table of Contents



ExhibitNumber
    
    Description10-K filed with the SEC on March 12, 2009, File No. 001-33452.10.29
    
    Long-term Purchase Agreement, dated December 22, 2008, among the Company, e2v, Inc. and e2v
Technologies (UK) Limited  Incorporated herein by reference to Exhibit 10.1 to the Companys
current report on Form 8-K filed with the SEC on December 30, 2008, File No. 001-33452.10.30
    
    Manufacture and Supply Agreement, dated January 13, 2009 and effective October 8, 2008, between
the Company and Siemens AG Healthcare Sector, Components & Vacuum Technology  Incorporated
herein by reference to Exhibit 10.1 to the Companys current report on Form 8-K filed with the
SEC on January 16, 2009, File No. 001-33452.10.31
    
    Amendment One to Manufacture and Supply Agreement, dated April 13, 2009, between the Company and
Siemens AG Healthcare Sector, Components & Vacuum Technology  Incorporated herein by reference
to Exhibit 10.1 to the Companys current report on Form 8-K filed with the SEC on April 13, 2009,
File No. 001-33452.10.32+
    
    Form of First Amendment to Employment Agreement, dated July 1, 2009, between the Company and
Brenda S. Furlow and Eric A. Schloesser  Incorporated herein by reference to Exhibit 10.33 to
the Companys annual report on Form 10-K filed with the SEC on March 11, 2010, File No.
001-33452.10.33
    
    Magnetron Subscription Agreement, dated April 24, 2009 and effective May 1, 2009, between the
Company and e2v, Inc. and e2v Technologies (UK) Limited  Incorporated herein by reference to
Exhibit 10.1 to the Companys current report on Form 8-K filed with the SEC on April 29, 2009,
File No. 001-33452.10.34+
    
    Employment Agreement, dated June 10, 2009 and effective June 22, 2009, between the Company and
Thomas E. Powell  Incorporated herein by reference to Exhibit 10.1 to the Companys current
report on Form 8-K filed with the SEC on June 11, 2009, File No. 001-33452.10.35+
    
    Form of First Amendment to Employment Agreement, dated July 1, 2009, between the Company and T.
Rockwell Mackie and Thomas E. Powell  Incorporated herein by reference to Exhibit 10.6 to the
Companys quarterly report on Form 10-Q filed with the SEC on August 6, 2009, File No. 001-33452.10.36+
    
    First Amendment to Employment Agreement, dated July 1, 2009, between the Company and Rafael L.
Vaello  Incorporated herein by reference to Exhibit 10.38 to the Companys annual report on
Form 10-K filed with the SEC on March 11, 2010, File No. 001-33452.10.37
    
    Magnetron Subscription Agreement (revised redaction), dated April 24, 2009 and effective May 1,
2009, between the Company and e2v, Inc. and e2v Technologies (UK) Limited  Incorporated herein
by reference to Exhibit 10.1 to the Companys current report on Form 8-K filed with the SEC on
October 28, 2009, File No. 001-33452.10.38
    
    Amended and Restated Equity Interest Transfer Agreement, dated November 18, 2009, between the
Company and Chengdu Twin-Peak Accelerator Technology Inc., Sichuan Nanguang Vacuum Technology
Incorporated Ltd. and Yao Chongguo   Incorporated herein by reference to Exhibit 2.1 to the
Companys current report on Form 8-K filed with the SEC on November 23, 2009, File No. 001-33452.10.39+
    
    Amended and Restated Employment Agreement, dated March 9, 2010, between the Company and Frederick
A. Robertson   Incorporated herein by reference to Exhibit 10.45 to the Companys annual report
on Form 10-K filed with the SEC on March 11, 2010, File No. 001-33452.10.40
    
    Termination of Avalon Agreement, dated May 28, 2010, between the company and Avalon Capital
Group, Inc., Avalon Technology, LLC and Avalon Portfolio, LLC  Incorporated herein by reference
to Exhibit 10.1 to the Companys current report on Form 8-K filed with the SEC on June 1, 2010,
File No. 001-33452.10.41 
    
    Amendment to Supply Agreement, dated September 10, 2010, between the Company and Hitachi Medical
Corporation  Incorporated herein by reference to Exhibit 10.1 to the Companys current report
on Form 8-K filed with the SEC on September 10, 2010, File No. 001-33452.10.42 
    
    Second Amended and Restated Loan Agreement, dated November 30, 2010, between the Company and M&I
Marshall & Ilsley Bank   Incorporated herein by reference to Exhibit 10.1 to the Companys
current report on Form 8-K filed with the SEC on December 2, 2010, File No. 001-33452.10.43 
    
    Second Amended and Restated Promissory Note, dated November 30, 2010, between the Company and M&I
Marshall & Ilsley Bank   Incorporated herein by reference to Exhibit 10.2 to the Companys
current report on Form 8-K filed with the SEC on December 2, 2010, File No. 001-33452.10.44+
    
    Second Amendment to Employment Agreement, dated as of March 6, 2011, by and between the Company
and Brenda S. Furlow  Incorporated by reference to Exhibit 10.1 to the Companys current report
of Form 8-K filed with the SEC on March 7, 2011, File No. 001-33452.
 24




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##### Table of Contents



ExhibitNumber
    
    Description21
    
    Subsidiaries of TomoTherapy Incorporated  Incorporated herein by reference to Exhibit 21 to the
Companys annual report on Form 10-K filed with the SEC on March 3, 2011, File No. 001-33452.23.1
    
    Consent of PricewaterhouseCoopers LLP, independent registered accounting firm  Incorporated
herein by reference to Exhibit 23.1 to the Companys annual report on Form 10-K filed with the
SEC on March 3, 2011, File No. 001-33452.23.2
    
    Consent of Grant Thornton LLP, independent registered public accounting firm  Incorporated
herein by reference to Exhibit 23.2 to the Companys annual report on Form 10-K filed with the
SEC on March 3, 2011, File No. 001-33452.31.1*
    
    Certification of Chief Executive Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 200231.2*
    
    Certification of Chief Financial Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 200232.1*
    
    Certification of Chief Executive Officer Pursuant to Section 906 of the Sarbanes-Oxley Act of 200232.2*
    
    Certification of Chief Financial Officer Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
 
 *
    
    Filed herewith
    
    Confidential treatment has been requested for portions of this
exhibit. These portions have been omitted from the corresponding
filing and submitted separately to the SEC.+
    
    Executive compensation plan or arrangement. 25




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##### Table of Contents



SIGNATURES
  By:
    /s/ Frederick A. RobertsonFrederick A. Robertson, M.D.Chief Executive Officer and PresidentDated: April 15, 2011  Name
    
    Position/s/ Frederick A. Robertson
    
    Chief Executive Officer, President and DirectorFrederick A. Robertson, M.D.
    
    (principal executive officer)/s/ Thomas E. Powell
    
    Chief Financial Officer and Treasurer (principalThomas E. Powell
    
    financial and accounting officer)*
    
    Chairman of the Board, DirectorT. Rockwell Mackie, Ph.D.*
    
    DirectorLance C. Balk*
    
    DirectorSam R. Leno*
    
    DirectorH. Jonathan McCloskey*
    
    DirectorJohn J. McDonough*
    
    DirectorCary J. Nolan*
    
    DirectorCarlos A. Perez*
    
    DirectorRoy T. Tanaka*
    
    DirectorFrances S. Taylor* /s/ Brenda S. Furlow
    
    Vice President, Corporate Secretary and General CounselBrenda S. Furlow, As Attorney-in-Fact
 26




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##### Table of Contents



EXHIBIT INDEX
 ExhibitNumber
    
    Description2.1
    
    Agreement and Plan of Merger, dated as of March 6, 2011, among Parent, Merger Sub and the Company
 Incorporated by referenced to Exhibit 2.1 to the Companys current report of Form 8-K filed
with the SEC on March 7, 2011, File No. 001-33452.3.1
    
    Amended and Restated Articles of Incorporation of the Company  Incorporated herein by reference
to Exhibit 3.1 to the Companys quarterly report on Form 10-Q filed with the SEC on November 7,
2008, File No. 001-33452.3.2
    
    Amended and Restated Bylaws of the Company  Incorporated herein by reference to Exhibit 3.2 to
the Companys quarterly report on Form 10-Q filed with the SEC on November 7, 2008, File No.
001-33452.4.1
    
    Form of the Companys Common Stock Certificate  Incorporated herein by reference to Exhibit 4.1
to Amendment No. 2 to the Companys registration statement on Form S-1 filed with the SEC on
April 16, 2007, File No. 333-140600.10.1
    
    Lease Agreement, dated January 26, 2005, between the Company and Old Sauk Trails Park Limited
Partnership  Incorporated herein by reference to Exhibit 10.13 to the Companys registration
statement on Form S-1 filed with the SEC on February 12, 2007, File No. 333-140600.10.2
    
    Lease Agreement, dated October 28, 2005, between the Company and Adelphia, LLC  Incorporated
herein by reference to Exhibit 10.14 to the Companys registration statement on Form S-1 filed
with the SEC on February 12, 2007, File No. 333-140600.10.3+
    
    Incentive Stock Option Plan, as amended, and forms of option agreements thereunder 
Incorporated herein by reference to Exhibit 10.16 to the Companys registration statement on Form
S-1 filed with the SEC on February 12, 2007, File No. 333-140600.10.4+
    
    2000 Stock Option Plan, as amended, and forms of option agreements thereunder  Incorporated
herein by reference to Exhibit 10.17 to the Companys registration statement on Form S-1 filed
with the SEC on February 12, 2007, File No. 333-140600.10.5+
    
    2002 Stock Option Plan, as amended, and forms of option agreements thereunder  Incorporated
herein by reference to Exhibit 10.18 to the Companys registration statement on Form S-1 filed
with the SEC on February 12, 2007, File No. 333-140600.10.6
    
    Standard Terms and Conditions of Sale  Incorporated herein by reference to Exhibit 10.19 to the
Companys registration statement on Form S-1 filed with the SEC on February 12, 2007, File No.
333-140600.10.7
    
    International Standard Terms and Conditions of Sale  Incorporated herein by reference to
Exhibit 10.20 to the Companys registration statement on Form S-1 filed with the SEC on February
12, 2007, File No. 333-140600.10.8
    
    Tomo Lifecycle Care and Partnership Terms and Conditions  Incorporated herein by reference to
Exhibit 10.21 to the Companys registration statement on Form S-1 filed with the SEC on February
12, 2007, File No. 333-140600.10.9
    
    Development and OEM Supply Agreement, dated January 27, 2003, between the Company and Analogic
Corporation  Incorporated herein by reference to Exhibit 10.11 to Amendment No. 2 to the
Companys registration statement on Form S-1 filed with the SEC on April 16, 2007, File No.
333-140600.10.10+
    
    2007 Equity Incentive Plan  Incorporated herein by reference to Exhibit 10.19 to Amendment No.
2 to the Companys registration statement on Form S-1 filed with the SEC on April 16, 2007, File
No. 333-140600.10.11+
    
    First Amendment to 2007 Equity Incentive Plan, dated May 1, 2009  Incorporated herein by
reference to Exhibit 99.1 to the Companys current report on Form 8-K filed with the SEC on May
5, 2009, File No. 001-33452.10.12+
    
    Second Amendment to 2007 Equity Incentive Plan, dated December 9, 2010  Incorporated herein by
reference to Exhibit 10.12 to the Companys annual report on Form 10-K filed with the SEC on
March 3, 2011, File No. 001-33452.10.13+
    
    2007 Employee Stock Purchase Plan, as amended  Incorporated herein by reference to Exhibit
10.20 to Amendment No. 2 to the Companys registration statement on Form S-1 filed with the SEC
on April 16, 2007, File No. 333-140600.10.14
    
    Form of Noncompetition Agreement  Incorporated herein by reference to Exhibit 10.27 to
Amendment No. 2 to the Companys registration statement on Form S-1 filed with the SEC on April
16, 2007, File No. 333-140600.
 27




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##### Table of Contents



ExhibitNumber
    
    Description10.15
    
    Form of Assignment of Inventions Agreement  Incorporated herein by reference to Exhibit 10.28
to Amendment No. 2 to the Companys registration statement on Form S-1 filed with the SEC on
April 16, 2007, File No. 333-140600.10.16
    
    Form of Confidentiality Agreement  Incorporated herein by reference to Exhibit 10.29 to
Amendment No. 2 to the Companys registration statement on Form S-1 filed with the SEC on April
16, 2007, File No. 333-140600.10.17
    
    License Agreement 98-0228, dated February 22, 1999, between the Company and Wisconsin Alumni
Research Foundation  Incorporated herein by reference to Exhibit 10.4 to Amendment No. 3 to the
Companys registration statement on Form S-1 filed with the SEC on April 19, 2007, File No.
333-140600.10.18
    
    Amendment to License Agreement 98-0228, dated April 16, 2007, between the Company and Wisconsin
Alumni Research Foundation  Incorporated herein by reference to Exhibit 10.31 to the Companys
registration statement on Form S-1 filed with the SEC on September 21, 2007, File No. 333-146219.10.19
    
    Amendment to License Agreement 98-0228, dated December 16, 2008, between the Company and
Wisconsin Alumni Research Foundation  Incorporated herein by reference to Exhibit 10.2 to the
Companys current report on Form 8-K filed with the SEC on December 30, 2008, File No. 001-33452.10.20
    
    Stock Purchase Agreement, dated April 25, 2008, between Compact Particle Acceleration Corporation
and its investors  Incorporated herein by reference to Exhibit 10.1 to the Companys current
report on Form 8-K filed with the SEC on April 28, 2008, File No. 001-33452.10.21
    
    Shareholder Agreement, dated April 25, 2008, between Compact Particle Acceleration Corporation
and its investors  Incorporated herein by reference to Exhibit 10.2 to the Companys current
report on Form 8-K filed with the SEC on April 28, 2008, File No. 001-33452.10.22
    
    Investors Rights Agreement, dated April 25, 2008, between Compact Particle Acceleration
Corporation and its investors  Incorporated herein by reference to Exhibit 10.3 to the
Companys current report on Form 8-K filed with the SEC on April 28, 2008, File No. 001-33452.10.23
    
    Limited Exclusive License Agreement, dated February 23, 2007, between the Company and Regents of
the University of California  Incorporated herein by reference to Exhibit 10.4 to the Companys
current report on Form 8-K filed with the SEC on April 28, 2008, File No. 001-33452.10.24
    
    Amendment One to Limited Exclusive License Agreement, dated April 8, 2008, between the Company
and Lawrence Livermore National Security, LLC  Incorporated herein by reference to Exhibit 10.5
to the Companys current report on Form 8-K filed with the SEC on April 28, 2008, File No.
001-33452.10.25
    
    Limited Exclusive Sublicense Agreement, dated April 25, 2008, between the Company and Compact
Particle Acceleration Corporation  Incorporated herein by reference to Exhibit 10.6 to the
Companys current report on Form 8-K filed with the SEC on April 28, 2008, File No. 001-33452.10.26
    
    Supply Agreement, dated June 25, 2008, between the Company and Hitachi Medical Corporation 
Incorporated herein by reference to Exhibit 10.1 to the Companys current report on Form 8-K
filed with the SEC on June 30, 2008, File No. 001-33452.10.27
    
    Form of Indemnification Agreement for Directors, Executive Officers, and Controller 
Incorporated herein by reference to Exhibit 10.3 to the Companys quarterly report on Form 10-Q
filed with the SEC on November 7, 2008, File No. 001-33452.10.28+
    
    Form of Employment Agreement, dated November 5, 2008, between the Company and Brenda S. Furlow
and Rafael L. Vaello  Incorporated herein by reference to Exhibit 10.37 to the Companys annual
report on Form 10-K filed with the SEC on March 12, 2009, File No. 001-33452.10.29
    
    Long-term Purchase Agreement, dated December 22, 2008, among the Company, e2v, Inc. and e2v
Technologies (UK) Limited  Incorporated herein by reference to Exhibit 10.1 to the Companys
current report on Form 8-K filed with the SEC on December 30, 2008, File No. 001-33452.10.30
    
    Manufacture and Supply Agreement, dated January 13, 2009 and effective October 8, 2008, between
the Company and Siemens AG Healthcare Sector, Components & Vacuum Technology  Incorporated
herein by reference to Exhibit 10.1 to the Companys current report on Form 8-K filed with the
SEC on January 16, 2009, File No. 001-33452.10.31
    
    Amendment One to Manufacture and Supply Agreement, dated April 13, 2009, between the Company and
Siemens AG Healthcare Sector, Components & Vacuum Technology  Incorporated herein by reference
to Exhibit 10.1 to the Companys current report on Form 8-K filed with the SEC on April 13, 2009,
File No. 001-33452.10.32+
    
    Form of First Amendment to Employment Agreement, dated July 1, 2009, between the Company and
Brenda S.
 28




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##### Table of Contents



ExhibitNumber
    
    DescriptionFurlow and Eric A. Schloesser  Incorporated herein by reference to Exhibit 10.33 to
the Companys annual report on Form 10-K filed with the SEC on March 11, 2010, File No.
001-33452.10.33
    
    Magnetron Subscription Agreement, dated April 24, 2009 and effective May 1, 2009, between the
Company and e2v, Inc. and e2v Technologies (UK) Limited  Incorporated herein by reference to
Exhibit 10.1 to the Companys current report on Form 8-K filed with the SEC on April 29, 2009,
File No. 001-33452.10.34+
    
    Employment Agreement, dated June 10, 2009 and effective June 22, 2009, between the Company and
Thomas E. Powell  Incorporated herein by reference to Exhibit 10.1 to the Companys current
report on Form 8-K filed with the SEC on June 11, 2009, File No. 001-33452.10.35+
    
    Form of First Amendment to Employment Agreement, dated July 1, 2009, between the Company and T.
Rockwell Mackie and Thomas E. Powell  Incorporated herein by reference to Exhibit 10.6 to the
Companys quarterly report on Form 10-Q filed with the SEC on August 6, 2009, File No. 001-33452.10.36+
    
    First Amendment to Employment Agreement, dated July 1, 2009, between the Company and Rafael L.
Vaello  Incorporated herein by reference to Exhibit 10.38 to the Companys annual report on
Form 10-K filed with the SEC on March 11, 2010, File No. 001-33452.10.37
    
    Magnetron Subscription Agreement (revised redaction), dated April 24, 2009 and effective May 1,
2009, between the Company and e2v, Inc. and e2v Technologies (UK) Limited  Incorporated herein
by reference to Exhibit 10.1 to the Companys current report on Form 8-K filed with the SEC on
October 28, 2009, File No. 001-33452.10.38
    
    Amended and Restated Equity Interest Transfer Agreement, dated November 18, 2009, between the
Company and Chengdu Twin-Peak Accelerator Technology Inc., Sichuan Nanguang Vacuum Technology
Incorporated Ltd. and Yao Chongguo   Incorporated herein by reference to Exhibit 2.1 to the
Companys current report on Form 8-K filed with the SEC on November 23, 2009, File No. 001-33452.10.39+
    
    Amended and Restated Employment Agreement, dated March 9, 2010, between the Company and Frederick
A. Robertson   Incorporated herein by reference to Exhibit 10.45 to the Companys annual report
on Form 10-K filed with the SEC on March 11, 2010, File No. 001-33452.10.40
    
    Termination of Avalon Agreement, dated May 28, 2010, between the company and Avalon Capital
Group, Inc., Avalon Technology, LLC and Avalon Portfolio, LLC  Incorporated herein by reference
to Exhibit 10.1 to the Companys current report on Form 8-K filed with the SEC on June 1, 2010,
File No. 001-33452.10.41 
    
    Amendment to Supply Agreement, dated September 10, 2010, between the Company and Hitachi Medical
Corporation  Incorporated herein by reference to Exhibit 10.1 to the Companys current report
on Form 8-K filed with the SEC on September 10, 2010, File No. 001-33452.10.42 
    
    Second Amended and Restated Loan Agreement, dated November 30, 2010, between the Company and M&I
Marshall & Ilsley Bank   Incorporated herein by reference to Exhibit 10.1 to the Companys
current report on Form 8-K filed with the SEC on December 2, 2010, File No. 001-33452.10.43 
    
    Second Amended and Restated Promissory Note, dated November 30, 2010, between the Company and M&I
Marshall & Ilsley Bank   Incorporated herein by reference to Exhibit 10.2 to the Companys
current report on Form 8-K filed with the SEC on December 2, 2010, File No. 001-33452.10.44+
    
    Second Amendment to Employment Agreement, dated as of March 6, 2011, by and between the Company
and Brenda S. Furlow  Incorporated by reference to Exhibit 10.1 to the Companys current report
of Form 8-K filed with the SEC on March 7, 2011, File No. 001-33452.21
    
    Subsidiaries of TomoTherapy Incorporated  Incorporated herein by reference to Exhibit 21 to the
Companys annual report on Form 10-K filed with the SEC on March 3, 2011, File No. 001-33452.23.1
    
    Consent of PricewaterhouseCoopers LLP, independent registered accounting firm  Incorporated
herein by reference to Exhibit 23.1 to the Companys annual report on Form 10-K filed with the
SEC on March 3, 2011, File No. 001-33452.23.2
    
    Consent of Grant Thornton LLP, independent registered public accounting firm  Incorporated
herein by reference to Exhibit 23.2 to the Companys annual report on Form 10-K filed with the
SEC on March 3, 2011, File No. 001-33452.31.1*
    
    Certification of Chief Executive Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 200231.2*
    
    Certification of Chief Financial Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 200232.1*
    
    Certification of Chief Executive Officer Pursuant to Section 906 of the Sarbanes-Oxley Act of 200232.2*
    
    Certification of Chief Financial Officer Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
 
 *
    
    Filed herewith
    
    Confidential treatment has been requested for portions of this
exhibit. These portions have been omitted from the corresponding
filing and submitted separately to the SEC.+
    
    Executive compensation plan or arrangement. 29