##### 



Exhibit 3.2
 AMENDED AND RESTATED
 ARTICLES OF INCORPORATION
OF
TOMOTHERAPY INCORPORATED
(Interim)
 TomoTherapy Incorporated Company
 ARTICLE I
 Name
 TomoTherapy Incorporated.
 ARTICLE II
 Purposes
  ARTICLE III
 Capital Stock
 COMMON STOCK
 Common Stock
 Preferred Stock
  Series A Preferred Stock
 Authorized Series A Preferred Shares Series A Preferred Stock
 1




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Series A Investment
Agreement
 Dividends
  Section 1.5(e)(ii) Section 1.5
  Liquidation, Dissolution or Winding Up
 Section 4.3(a) Section 5.3(a) provided Series A Liquidation Preference Payment Liquidation Preference Payments 2
       Remaining Net Assets Common Equivalent Valuation
       Section 1.5(g) Section 1.3 provided, however Section 1.5(g) Section 1.3
 3
        Voting Power Section 1.8 Section 1.5
 Conversion Rights
 General Section
1.5 Section 1.5(c)
 Mandatory Conversion Following Underwritten Public Offering or Vote of Holders of
Series A Preferred Stock
 Section 1.5(e)(ii) Section 1.5(f) (g) Section 1.5(a) Section
1.5(a) Sections 4.5(e)(ii) (f) (g) Sections 5.5(e)(ii) (f) (g)
 4




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Section 1.5(b)(i)
 Series A Applicable Conversion Rate Series A Applicable Conversion Rate Section
1.5(d)
 Series A Applicable Conversion Value Section 1.5(e)
 Adjustments to Series A Applicable Conversion Value
 Upon Issuance or Sale of Common Stock
   Section 1.5
 Article VIII Section
1.5 Section 1.5
 Section 1.5(e)(i)
 5




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Section 1.5(e)(i)
 Net Consideration Per Share
  Section 1.5(e)(i) Section 1.5(e)(i)
 Section 1.5(e)(i) Section
1.5(e)(ii)
 Upon Extraordinary Common Stock Event Section 1.5(e)(i)
 Extraordinary Common Stock Event
 6




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Recapitalization or Reclassification Section 1.5 Section 1.5
 Capital Reorganization, Merger or Sale of Assets Section
1.5 Section 1.5 Section 1.5
 Section
1.5(g) Section 1.5(g) Section 1.3(b)
 Determination of Adjustments
 Exercise of Conversion Privilege Conversion Date
 7




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Section 1.5 Section 1.5(j)
 Cash in Lieu of Fractional Shares
 Partial Conversion
 Reservation of Common Stock
 No Reissuance of Convertible Series A Preferred Stock
 Restriction and Limitations Sections 2.7 or 3.7
 No Dilution or Impairment
 8




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Notices of Record Date
     Rank
 Series B Preferred Stock
 Authorized Series B Preferred Shares Series B Preferred Stock
 Dividends
  Section 2.5(e)(ii)
 9




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Section 2.5
  Liquidation, Dissolution or Winding Up
 Section 4.3(a) Section 5.3(a) provided Series B
Liquidation Preference Payment Liquidation Preference
Payments Remaining Net Assets Common Equivalent Valuation
   10




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Section 2.5(g) Section 2.3 provided, however Section 2.5(g) Section 2.3
  Voting Power Section 2.8 Section 2.5
 Conversion Rights
 General Section
2.5 Section 2.5(c)
 11




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Mandatory Conversion Following Underwritten Public Offering or Vote of Holders of
Series B Preferred Stock
 Section 2.5(e)(ii) Section 2.5(f) (g) Section 2.5(a) Section
2.5(a) Sections 4.5(e)(ii) (f) (g) Sections 5.5(e)(ii) (f) (g)
 Section 2.5(b)(i)
 Applicable Series B Conversion Rate Applicable Series B Conversion Rate Section
2.5(d)
 Applicable Series B Conversion Value Section 2.5(e)
 Adjustments to Applicable Series B Conversion Value
 Upon Issuance or Sale of Common Stock
 12




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Section 2.5
 Article VIII Section
2.5 Section 2.5
 Section 2.5(e)(i) Section 2.5(e)(i)
 Net Consideration Per Share
 13




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Section 2.5(e)(i) Section 2.5(e)(i)
 Section 2.5(e)(i) Section
2.5(e)(ii)
 Upon Extraordinary Common Stock Event Section 2.5(e)(i)
 Extraordinary Common Stock Event
 Recapitalization or Reclassification Section 2.5 Section 2.5
 Capital Reorganization, Merger or Sale of Assets Section
2.5 Section 14
       2.5 Section
2.5
 Section
2.5(g) Section 2.5(g) Section 2.3(b)
 Determination of Adjustments
 Exercise of Conversion Privilege Conversion Date Section 2.5 Section 2.5(j)
 Cash in Lieu of Fractional Shares
 Partial Conversion
 15




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Reservation of Common Stock
 No Reissuance of Convertible Series B Preferred Stock
 Restriction and Limitations
        16




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Section 2.7
 No Dilution or Impairment
 Notices of Record Date
     Rank
 Series C Preferred Stock
 Authorized Series C Preferred Shares Series C Preferred Stock
 17




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Dividends
  Section 3.5(e)(ii) Section 3.5
  Liquidation, Dissolution or Winding Up
 Section 4.3(a) Section 5.3(a) provided Series C
Liquidation Preference Payment Liquidation Preference Payments
 18




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##### 



Remaining Net Assets Common Equivalent Valuation
       Section 3.5(g) Section 3.3 provided, however Section 3.5(g) Section 3.3
  19




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Voting Power Section 3.8 Section 3.5
 Conversion Rights
 General Section
3.5 Section 3.5(c)
 Mandatory Conversion Following Underwritten Public Offering or Vote of Holders of
Series C Preferred Stock
 Section 3.5(e)(ii) Section 3.5(f) (g) Section 3.5(a) Section
3.5(a) Sections 4.5(e)(ii) (f) (g) Sections 5.5(e)(ii) (f) (g)
 Section 3.5(b)(i)
 20




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Applicable Series C Conversion Rate Applicable Series C Conversion Rate Section
3.5(d)
 Applicable Series C Conversion Value Section 3.5(e)
 Adjustments to Applicable Series C Conversion Value
 Upon Issuance or Sale of Common Stock
   Section 3.5
 Article VIII Section
3.5 Section 3.5
 Section 3.5(e)(i)
 21




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Section
3.5(e)(i)
 Net Consideration Per Share
  Section 3.5(e)(i) Section 3.5(e)(i)
 Section 3.5(e)(i) Section
3.5(e)(ii)
 Upon Extraordinary Common Stock Event Section 3.5(e)(i)
 Extraordinary Common Stock Event
 22




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##### 



Recapitalization or Reclassification Section 3.5 Section 3.5
 Capital Reorganization, Merger or Sale of Assets Section
3.5 Section 3.5 Section 3.5
 Section
3.5(g) Section 3.5(g) Section 3.3(b)
 Determination of Adjustments
 Exercise of Conversion Privilege Conversion Date Section 3.5 Section 3.5(j)
 23




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Cash in Lieu of Fractional Shares
 Partial Conversion
 Reservation of Common Stock
 No Reissuance of Convertible Series C Preferred Stock
 Restriction and Limitations
     24




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##### 



Section 3.7
 No Dilution or Impairment
 Notices of Record Date
     25




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##### 



Rank
 Series D Preferred Stock
 Authorized Series D Preferred Shares Series D Preferred Stock
 Dividends
  Section 4.5(e)(ii) Section 4.5
  Liquidation, Dissolution or Winding Up
  26




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Section 5.3(a) Section 4.3(a) Series D
Liquidation Preference Amount Total Series D Liquidation
Preference Payment. Remaining Net Assets Common Equivalent Valuation
 Section 4.5(g) Section 4.3 provided, however Section 4.5(g) Section 4.3
  Voting Power Section 4.8 Section 4.5
 27




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Conversion Rights
 General Section
4.5 Section 4.5(c)
 Mandatory Conversion Following Underwritten Public Offering or Vote of Holders of
Series D Preferred Stock
 Section 4.5(e)(ii) Section 4.5(f) (g) Section 4.5(a) Section
4.5(a) Sections 4.5(e)(ii) (f) (g)
 Section 4.5(b)(i)
 Applicable Series D Conversion Rate Applicable Series D Conversion Rate Section
4.5(d)
 Applicable Series D Conversion Value Section 4.5(e)
 28




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Adjustments to Applicable Series D Conversion Value
 Upon Issuance or Sale of Common Stock
   Section 4.5
 Article VIII Section
4.5 Section 4.5
 Section 4.5(e)(i) Section 4.5(e)(i)
 29




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Net Consideration Per Share
  Section 4.5(e)(i) Section 4.5(e)(i)
 Section 4.5(e)(i) Section
4.5(e)(ii)
 Upon Extraordinary Common Stock Event Section 4.5(e)(i)
 Extraordinary Common Stock Event
 Recapitalization or Reclassification Section 4.5 Section 4.5
 Capital Reorganization, Merger or Sale of Assets Section
4.5
 30




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Section 4.5 Section 4.5
 Section
4.5(g) Section 4.5(g) Section 4.3(b)
 Determination of Adjustments
 Exercise of Conversion Privilege Conversion Date Section 4.5 Section 4.5(j)
 Cash in Lieu of Fractional Shares
 31




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Partial Conversion
 Reservation of Common Stock
 No Reissuance of Convertible Series D Preferred Stock
 Restriction and Limitations
 2 3
        32




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Section 4.7
 No Dilution or Impairment
 Notices of Record Date
     Rank
 Series E Preferred Stock
 Authorized Series E Preferred Shares Series E Preferred Stock
 Dividends
  33




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Section 5.5(e)(ii) Section 5.5
  Liquidation, Dissolution or Winding Up
 Series E Liquidation Preference Amount Total Series E
Liquidation Preference Payment. Remaining
Net Assets Common Equivalent
Valuation
 34




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Section 5.5(g) Section 5.3 provided however Section 5.5(g) Section 5.3
  Voting Power Section 5.8 Section 5.5
 Conversion Rights
 General Section
5.5 Section 5.5(c)
 Mandatory Conversion Following Underwritten Public Offering or Vote of Holders of
Series E Preferred Stock
 Section 5.5(e)(ii) Section 5.5(f) (g)
 35




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Section 5.5(a) Section 5.5(a)
 Section 5.5(b)(i)
 Applicable Series E Conversion Rate Applicable Series E Conversion Rate Section
5.5(d)
 Applicable Series E Conversion Value Section 5.5(e)
 Adjustments to Applicable Series E Conversion Value
 Upon Issuance or Sale of Common Stock
   Section 5.5
 36




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Article VIII Section
5.5 Section 5.5
 Section 5.5(e)(i) Section 5.5(e)(i)
 Net Consideration Per Share
  Section 5.5(e)(i) Section 5.5(e)(i)
 Section 5.5(e)(i) Section
5.5(e)(ii)
 Upon Extraordinary Common Stock Event
 37




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Section 5.5(e)(i)
 Extraordinary Common Stock Event
 Recapitalization or Reclassification Section 5.5 Section 5.5
 Capital Reorganization, Merger or Sale of Assets Section
5.5 Section 5.5 Section 5.5
 Series E Section
5.5(g) Section 5.5(g) Section 5.3(b)
 Determination of Adjustments
 38




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Exercise of Conversion Privilege Conversion Date Section 5.5 Section 5.5(j)
 Cash in Lieu of Fractional Shares
 Partial Conversion
 Reservation of Common Stock
 No Reissuance of Convertible Series E Preferred Stock
 Restriction and Limitations
 2 3
 39




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Section 5.7
 2 3
      No Dilution or Impairment
 40




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Notices of Record Date
     Rank
 ARTICLE V
 Registered Office and Agent
  
 41




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TomoTherapy Incorporated
 Shawn D. Guse, Vice President and General CounselDated: May 7, 2007  
 42