Exhibit 3.2
 AMENDED AND RESTATED BYLAWS
 OF
 TOMOTHERAPY INCORPORATED




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INDEX TO AMENDED AND RESTATED BYLAWS
OF
TOMOTHERAPY INCORPORATED
 Section
    
    PageARTICLE 1 IDENTIFICATION
    
    
    11.1 Name
    
    
    11.2 Principal and Business Offices
    
    
    11.3 Registered Agent and Office
    
    
    11.4 Place of Keeping Corporate Records
    
    
    1ARTICLE 2 SHAREHOLDERS
    
    
    12.1 Annual Meeting
    
    
    12.2 Special Meetings
    
    
    12.3 Place of Meeting
    
    
    22.4 Notice of Meetings
    
    
    22.5 Waiver of Notice
    
    
    22.6 Fixing of Record Date
    
    
    22.7 Voting List
    
    
    32.8 Quorum and Voting Requirements
    
    
    32.9 Order of Business at Meetings
    
    
    42.10 Proxies
    
    
    42.11 Voting of Shares
    
    
    42.12 Voting of Shares by Certain Holders
    
    
    52.13 Action Without a Meeting
    
    
    62.14 Nominations and Proposals by Shareholders
    
    
    6ARTICLE 3 BOARD OF DIRECTORS
    
    
    93.1 General Powers
    
    
    93.2 Election
    
    
    93.3 Number, Tenure, and Qualifications
    
    
    103.4 Regular Meetings
    
    
    103.5 Special Meetings
    
    
    103.6 Meetings by Electronic Means of Communication
    
    
    103.7 Notice of Meetings; Waiver of Notice
    
    
    103.8 Quorum Requirement
    
    
    113.9 Voting Requirement
    
    
    113.10 Conduct of Meetings
    
    
    113.11 Vacancies
    
    
    113.12 Compensation and Expenses
    
    
    123.13 Directors Assent
    
    
    123.14 Committees
    
    
    123.15 Action Without a Meeting
    
    
    13




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Section
    
    PageARTICLE 4 OFFICERS
    
    
    134.1 Number and Titles
    
    
    134.2 Appointment, Tenure, and Compensation
    
    
    134.3
Additional Officers, Agents, Etc.
    
    
    134.4 Removal
    
    
    134.5 Resignations
    
    
    134.6 Vacancies
    
    
    144.7 Powers, Authority and Duties
    
    
    144.8 The Chairperson of the Board
    
    
    144.9 The President
    
    
    144.10 The Vice-Presidents
    
    
    154.11 The Secretary
    
    
    154.12 The Assistant Secretaries
    
    
    154.13 The Treasurer
    
    
    164.14 The Assistant Treasurers
    
    
    16ARTICLE 5 CONTRACTS, LOANS, CHECKS AND DEPOSITS
    
    
    175.1 Contracts
    
    
    175.2 Loans
    
    
    175.3 Checks,
Drafts, Etc.
    
    
    175.4 Deposits
    
    
    17ARTICLE 6 VOTING OF SECURITIES OWNED BY THE CORPORATION
    
    
    176.1 Authority to Vote
    
    
    176.2 Proxy Authorization
    
    
    17ARTICLE 7 CONTRACTS BETWEEN THE CORPORATION AND RELATED PERSONS
    
    
    18ARTICLE 8 CERTIFICATES FOR SHARES AND THEIR TRANSFER
    
    
    188.1 Certificates for Shares
    
    
    188.2 Facsimile Signatures
    
    
    198.3 Signature by Former Officer
    
    
    198.4 Consideration for Shares
    
    
    198.5 Transfer of Shares
    
    
    198.6 Restrictions on Transfer
    
    
    198.7 Lost, Destroyed, or Stolen Certificates
    
    
    20ARTICLE 9 INSPECTION OF RECORDS BY SHAREHOLDERS
    
    
    209.1 Inspection of Bylaws
    
    
    209.2 Inspection of Other Records
    
    
    20ARTICLE 10 DISTRIBUTIONS AND SHARE ACQUISITIONS
    
    
    20ARTICLE 11 INDEMNIFICATION
    
    
    21ARTICLE 12 AMENDMENTS
    
    
    2112.1 By Shareholders
    
    
    2112.2 By Directors
    
    
    21ARTICLE 13 SEAL
    
    
    21




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ARTICLE 1
 IDENTIFICATION
 Name
 Principal and Business Offices
 Registered Agent and Office
 Place of Keeping Corporate Records
 ARTICLE 2
 SHAREHOLDERS
 Annual Meeting
 Special Meetings Section 2.14(c) Section 2.4
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Place of Meeting
 Notice of Meetings Section 2.4
 Waiver of Notice
 Fixing of Record Date Section 2.2
 (a)
    
    With respect to an annual shareholders meeting or any special shareholders
meeting called by the board or any person specifically authorized by the board or these
bylaws to call a meeting, at the close of business on the day before the first notice
is delivered to shareholders;(b)
    
    With respect to a special shareholders meeting demanded by the shareholders,
on the date the first shareholder signs the demand;(c)
    
    With respect to actions taken in writing without a meeting (pursuant to
Section 2.13 of these bylaws), on the date the first shareholder signs a
consent;
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(d)
    
    With respect to determining shareholders entitled to a share dividend, on the
date the board authorizes the share dividend;(e)
    
    With respect to determining shareholders entitled to a distribution (other than
a distribution involving a repurchase or reacquisition of shares), on the date the
board authorizes the distribution; and(f)
    
    With respect to any other matter for which such a determination is required, as
provided by law.
  Voting List
 Quorum and Voting Requirements Section 3.2
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Order of Business at Meetings
  (a)
    
    Roll call;(b)
    
    Appointment of inspectors of election, if requested;(c)
    
    Proof of proper notice of meeting or receipt of waiver of notice;(d)
    
    Approval of minutes of preceding meeting, unless dispensed with by unanimous
consent;(e)
    
    Board of directors report, if any;(f)
    
    Officers reports, if any;(g)
    
    Committee reports, if any;(h)
    
    Election of directors, if necessary;(i)
    
    Unfinished business, if any; and(j)
    
    New business, if any.
 Section 2.8
 Proxies
 Voting of Shares
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Voting of Shares by Certain Holders
 (a)
    
    Other Corporations. Shares standing in another corporations name may
be voted either in person or by proxy, by the other corporations president or any
other officer appointed by the president. A proxy appointment executed by any principal
officer of the other corporation or such an officers assistant shall be conclusive
evidence of the signers authority to act, in the absence of express notice to this
corporation, given in writing to this corporations secretary, or other officer or
agent of this corporation authorized to tabulate votes, of the designation of some
other person by the other corporations board of directors or bylaws.(b)
    
    Legal Representatives and Fiduciaries. Shares held by a personal
representative, administrator, executor, guardian, conservator, trustee in bankruptcy,
receiver, or assignee for creditors, in a fiduciary capacity, may be voted by the
fiduciary, either in person or by proxy, without transferring the shares into his or
her name, provided that there is filed with the secretary, before or at the time of the
meeting, proper evidence of the fiduciarys incumbency and the number of shares held.
Shares standing in a fiduciarys name may be voted by him or her, either in person or
by proxy. A proxy appointment executed by a fiduciary shall be conclusive evidence of
the fiduciarys authority to give the proxy appointment, in the absence of express
notice to the corporation, given in writing to the secretary or other officer or agent
of the corporation authorized to tabulate votes, that this manner of voting is
expressly prohibited or otherwise directed by the document creating the fiduciary
relationship.(c)
    
    Pledgees. A shareholder whose shares are pledged shall be entitled to
vote the shares until they have been transferred into the pledgees name, and
thereafter the pledgee shall be entitled to vote the shares so transferred.(d)
    
    Treasury Stock and Subsidiaries. Neither treasury shares, nor shares
held by another corporation if a majority of the shares entitled to vote for the
election of directors of such other corporation is held by this corporation, shall be
voted at any meeting or counted in determining the total number of outstanding shares
entitled to vote, but shares of its own issue held by this corporation in a fiduciary
capacity, or held by such other corporation in a fiduciary capacity, may be voted and
shall be counted in determining the total number of outstanding shares entitled to
vote.(e)
    
    Minors. Shares held by a minor may be voted by the minor in person or
by proxy appointment, and no such vote shall be subject to disaffirmance or avoidance
unless before the vote the secretary or other officer or agent of the corporation
authorized to tabulate votes has received written notice or has actual knowledge that
the shareholder is a minor.
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(f)
    
    Incompetents and Spendthrifts. Shares held by an incompetent or
spendthrift may be voted by the incompetent or spendthrift in person or by proxy
appointment, and no such vote shall be subject to disaffirmance or avoidance unless
before the
vote the secretary or other officer or agent of the corporation authorized to
tabulate votes has actual knowledge that the shareholder has been adjudicated an
incompetent or spendthrift or actual knowledge that judicial proceedings for
appointment of a guardian have been filed.(g)
    
    Joint Tenants. Shares registered in the names of two or more
individuals who are named in the registration as joint tenants may be voted in person
or by proxy signed by one or more of the joint tenants if either (1) no other joint
tenant or his or her legal representative is present and claims the right to
participate in the voting of the shares or before the vote files with the secretary or
other officer or agent of the corporation authorized to tabulate votes a contrary
written voting authorization or direction or written denial of authority of the joint
tenant present or signing the proxy appointment proposed to be voted, or (2) all other
joint tenants are deceased and the secretary or other officer or agent of the
corporation authorized to tabulate votes has no actual knowledge that the survivor has
been adjudicated not to be the successor to the interests of those deceased.
 Action Without a Meeting
 Nominations and Proposals by Shareholders
 (a)
    
    Annual Meetings of Shareholders.
 Section 2.14(a) Section 2.14(a)
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Section 2.14(a)(1)(C) Section 2.14(a) Section 2.14(c)(1)
 Section 2.14(a) Section
2.14(a)
 Special Meetings of Shareholders Section 2.14(b) Section 2.14(b) Section 2.14(c)(1)
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General
 Section 2.14(a) (b) Section 2.2 Section 2.14(c)(1)
 Section 2.14 Section 2.14 Section 2.14 Section 2.14
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Section 2.14 Section 2.2 Section 2.14 Section 2.14 Section 2.14
 Section 2.14
 Section 2.14 Section
2.14 Section 2.14
 ARTICLE 3
 BOARD OF DIRECTORS
 General Powers
 Election Section 2.14
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Number, Tenure, and Qualifications
 Regular Meetings
 Special Meetings
 Meetings by Electronic Means of Communication
 Notice of Meetings; Waiver of Notice Section 3.4 forty-eight
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Quorum Requirement Section
3.3 Section 3.14 Article 7
 Voting Requirement Section 3.14 Article 7 Article 11
 Conduct of Meetings Section 4.10
 Vacancies
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Compensation and Expenses
 Directors Assent
 Committees Section 3.9
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Action Without a Meeting
 ARTICLE 4
 OFFICERS
 Number and Titles
 Appointment, Tenure, and Compensation
 Additional Officers, Agents, Etc Section 4.1
 Removal
 Resignations
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Vacancies
 Powers, Authority and Duties Article 4
 The Chairperson of the Board
 The President Section 4.8
 (a)
    
    Superintend and manage the corporations business;(b)
    
    Coordinate and supervise the work of its other officers (except the chairperson
of the board);(c)
    
    Employ, direct, fix the compensation of, discipline, and discharge its
employees;(d)
    
    Employ agents, professional advisors, and consultants;(e)
    
    Perform all functions of a general manager of the corporations business;(f)
    
    Have authority to sign, execute, and deliver in the corporations name all
instruments either when specifically authorized by the board of directors or when
required or deemed necessary or advisable by the president in the ordinary conduct of
the corporations normal business, except in cases where the signing and execution of
the instruments shall be expressly delegated by these bylaws or by the board to some
other officer(s) or agent(s) of the corporation or shall be required by law or
otherwise to be signed or executed by some other officer or agent; and(g)
    
    In general, perform all duties incident to the office of the president and such
other duties as from time to time may be assigned to him or her by the board of
directors.
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The Vice-Presidents vice-president,
 The Secretary
 (a)
    
    Keep any minutes of the shareholders and of the board of directors and its
committees in one or more books provided for that purpose;(b)
    
    See that all notices are duly given in accordance with these bylaws or as
required by law;(c)
    
    Be custodian of the corporations corporate records and see that the books,
reports, statements, certificates, and all other documents and records required by law
are properly kept and filed;(d)
    
    Have charge, directly or through such transfer agent or agents and registrar or
registrars as the board of directors may appoint, of the issue, transfer, and
registration of certificates for shares in the corporation and of the records thereof,
such records to be kept in such manner as to show at any time the number of shares in
the corporation issued and outstanding, the manner in which and time when such shares
were paid for, the names and addresses of the shareholders of record, the numbers and
classes of shares held by each, and the time when each became a shareholder;(e)
    
    Exhibit at reasonable times upon the request of any director the records of the
issue, transfer, and registration of the corporations share certificates, at the place
where those records are kept, and have these records available at each shareholders
meeting; and(f)
    
    In general, perform all duties incident to the office of the secretary and such
other duties as from time to time may be assigned to him or her by the board of
directors or the president.
 The Assistant Secretaries
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The Treasurer
 (a)
    
    Have charge and custody of, and be responsible for, all of the corporations
funds and securities; receive and give receipts for monies due and payable to the
corporation from any source whatsoever; deposit all such monies in the corporations
name in such banks, financial institutions, trust companies, or other depositories as
shall be selected in accordance with the provisions of Section 5.4 of these
bylaws; cause such funds to be disbursed by checks or drafts on the corporations
authorized depositories, signed as the board of directors may require; and be
responsible for the accuracy of the amounts of, and cause to be preserved proper
vouchers for, all monies disbursed;(b)
    
    Have the right to require from time to time reports or statements giving such
information as he or she may desire with respect to any and all of the corporations
financial transactions from the officers, employees, or agents transacting the same;(c)
    
    Keep or cause to be kept, at the corporations principal office or such other
office or offices as the board of directors shall from time to time designate, correct
records of the corporations funds, business, and transactions, and exhibit those
records to any director of the corporation upon request at that office;(d)
    
    Deliver to the board of directors, the chairperson of the board, or the
president whenever requested an account of the corporations financial condition and of
all his or her transactions as treasurer, and as soon as possible after the close of
each fiscal year, make or cause to be made and submit to the board a like report for
that fiscal year;(e)
    
    At each annual shareholders meeting or the meeting held in lieu thereof,
furnish copies of the corporations most current financial statement to the
shareholders and answer questions that may be raised regarding the statement; and(f)
    
    In general, perform all duties incident to the office of treasurer and such
other duties as from time to time may be assigned to him or her by the board of
directors or the president.
  The Assistant Treasurers
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ARTICLE 5
 CONTRACTS, LOANS, CHECKS AND DEPOSITS
 Contracts
 Loans
 Checks, Drafts, Etc
 Deposits
 ARTICLE 6
 VOTING OF SECURITIES OWNED BY THE CORPORATION
 Authority to Vote
 Proxy Authorization
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ARTICLE 7
 CONTRACTS BETWEEN THE CORPORATION AND RELATED PERSONS
     Article 7
 ARTICLE 8
 CERTIFICATES FOR SHARES AND THEIR TRANSFER
 Certificates for Shares Section 8.7
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Facsimile Signatures
 Signature by Former Officer
 Consideration for Shares
 Transfer of Shares
 Restrictions on Transfer
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Lost, Destroyed, or Stolen Certificates
 ARTICLE 9
 INSPECTION OF RECORDS BY SHAREHOLDERS
 Inspection of Bylaws
 Inspection of Other Records
 ARTICLE 10
 DISTRIBUTIONS AND SHARE ACQUISITIONS
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ARTICLE 11
 INDEMNIFICATION
  ARTICLE 12
 AMENDMENTS
 By Shareholders
 By Directors
 ARTICLE 13
 SEAL
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