Document:

EMPLOYMENT AGREEMENT DATED NOVEMBER 5, 2008

Exhibit 10.37

EMPLOYMENT AGREEMENT

(Non CEO)

THIS AGREEMENT is executed as of this 5th day of November, 2008, by and between TomoTherapy
Incorporated, a Wisconsin corporation (the “Company”), and Brenda S. Furlow, an individual
(“Employee”).

RECITALS

     The Company desires to employ Employee, and Employee desires to be employed by or continued to
be employed by the Company, on the terms and conditions set forth herein.

     The parties believe it is in their best interests to make provision for certain aspects of
their relationship during and after the period in which Employee is employed by the Company.

     NOW, THEREFORE, in consideration of the premises and the mutual agreements and covenants
contained herein, and for other good and valuable consideration, the receipt and sufficiency of
which is hereby acknowledged by the Company and Employee,

     IT IS HEREBY AGREED AS FOLLOWS:

ARTICLE I

EMPLOYMENT

     1.1 Term of Employment. The Company employs Employee, and Employee accepts employment by the
Company, for the period commencing on the date hereof and ending on March 31, 2009, subject to
earlier termination as hereinafter set forth in Article III (the “Employment Term”).
Following the expiration of the Employment Term, the Employment Term shall be automatically renewed
for successive one-year periods (collectively, the “Renewal Terms”; individually, a
“Renewal Term”) unless, at least 60 days prior to the expiration of the Employment Term or
the then current Renewal Term, either party provides the other with a written notice of intention
not to renew, in which case Employee’s employment with the Company, and the Company’s obligations
hereunder shall terminate as of the end of the Employment Term or said Renewal Term, as applicable,
except to the extent specifically provided herein. If the Employment Term is renewed, the terms of
this Agreement during such Renewal Term shall be the same as the terms in effect immediately prior
to such renewal, subject to any such changes or modifications as mutually may be agreed between the
parties as evidenced in a written instrument signed by both the Company and Employee.

     1.2 Position and Duties. Employee shall be employed in the position of Vice President, General
Counsel & Corporate Secretary, and shall be subject to the authority of, and shall report to, the
Company’s Chief Executive Officer. Employee’s duties and responsibilities shall include all those
customarily attendant to the position of Vice President, General Counsel & Corporate Secretary, and
such other duties and responsibilities as may be assigned by the Company’s Chief Executive Officer.
Employee shall devote Employee’s entire business time, loyalty, attention and energies exclusively
to the business interests of the Company while employed by the Company, and shall perform his
duties and responsibilities diligently and to the best of his ability.

 

 

ARTICLE II

COMPENSATION AND OTHER BENEFITS

     2.1 Base Salary. The Company shall pay Employee a salary at the annual rate of $201,500
(“Base Salary”), payable in accordance with the normal payroll practices of the Company.

     2.2 Performance Bonus. Employee will be eligible to earn an annual performance based bonus for
that portion of each full calendar year during which Employee is employed by the Company (a
“Bonus Year”), the terms and conditions of which as well as Employee’s entitlement thereto
shall be determined annually in the sole discretion of the Company’s Board of Directors or an
authorized committee thereof (the “Performance Bonus”). Employee must commence employment
with the Company before October 1 of the Bonus Year in order to be eligible for a Performance Bonus
for that Bonus Year. Any Performance Bonus payable hereunder shall be paid following the Bonus
Year not later than the earlier of (i) 30 days following the Company’s receipt of its annual
audited financial report or (ii) March 15 of the year following the Bonus Year.

     2.3 Benefit Plans. Employee will be eligible to participate in the Company’s retirement plans
that are qualified under Section 401(a) of the Internal Revenue Code of 1986, as amended (“Code”),
and in the Company’s welfare benefit plans that are generally applicable to all executive employees
of the Company (the “Plans”), in accordance with the terms and conditions thereof. The
Company intends to provide Employee with: (a) portable term life insurance with a death benefit
equal to twice the sum of Employee’s current Base Salary and target Performance Bonus; provided,
however, that the minimum benefit shall equal at least $500,000; and (b) long-term disability
insurance with an annual benefit equal to at least 75% of the sum of Employee’s Base Salary and
target Performance Bonus. Both the term life insurance and long-term disability insurance are,
however, subject to the underwriting process. To the extent that the costs of such coverages
materially exceed the average of such costs for other executives at the Company, the Company
reserves the right to modify the scope of coverage for Employee, or not offer it at all.

     2.4 Expenses. The Company shall reimburse Employee for all reasonable expenses incurred in the
course of the performance of Employee’s duties and responsibilities pursuant to this Agreement and
consistent with the Company’s policies with respect to travel, entertainment and miscellaneous
expenses, and the requirements with respect to the reporting of such expenses.

     2.5 Vacation. Employee shall be entitled to a maximum of four weeks of vacation in any calendar year in
accordance with the Company’s general vacation policies for similarly situated executive employees.

ARTICLE III

TERMINATION

     3.1 Right to Terminate; Automatic Termination.

          (a) Termination by Company Without Cause. Since Employee is an at-will employee, subject to
Section 3.2, the Company may terminate Employee’s employment and all of the obligations under this
Agreement at any time and for any reason.

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          (b) Termination by Employee for Good Reason. Subject to Section 3.2, Employee may terminate
his employment obligation hereunder for “Good Reason” (as hereinafter defined) if Employee gives
written notice thereof to the Company (which notice shall specify the grounds upon which such
notice is given) within 90 days of the initial occurrence of a “Good Reason” event and the Company
fails, within 90 days of receipt of such notice, to cure or rectify the grounds for such Good
Reason termination set forth in such notice. If the Company fails to so cure or rectify, the
Employee’s termination of employment shall not be deemed for “Good Reason” unless the Employee
terminates employment within one year of the initial occurrence of Good Reason. “Good Reason”
shall mean any of the following: (i) a material reduction of the Employee’s duties and
responsibilities hereunder; (ii) a material adverse change in the working conditions of the
Employee including, without limitation, relocation of Employee’s principal workplace over 50 miles
from the Company’s existing workplace, without the consent of Employee; or (iii) the Company’s
material breach of the Agreement.

          (c) Termination by Company For Cause. Subject to Section 3.2, the Company may terminate
Employee’s employment and all of the Company’s obligations under this Agreement at any time for
"Cause” (as defined below) by giving notice to Employee stating the basis for such termination,
effective immediately upon giving such notice or at such other time thereafter as the Company may
designate. “Cause” shall mean any of the following: (i) Employee has materially breached this
Agreement or any other agreement to which Employee and the Company are parties or has materially
breached any other obligation or duty owed to the Company, which material breach remains uncured
for 30 days after Employee receives notice thereof from the Chief Executive Officer; (ii) Employee
has committed gross negligence, willful misconduct or any material violation of law or the
Company’s Comprehensive Corporate Compliance Program in the performance of Employee’s duties to the
Company; (iii) Employee has engaged in any willful misconduct likely to result in material
discredit to or material loss of business, reputation or goodwill of the Company; (iv) Employee has
failed to follow in any material respect lawful instructions from the officer or body to whom
Employee reports concerning the operations or business of the Company, which
material failure to follow lawful instructions remains uncured for 30 days after Employee receives
notice thereof from the Chief Executive Officer; (v) Employee has been convicted of, or pled nolo
contendere to a felony; (vi) Employee has misappropriated funds or property of the Company; or
(vii) Employee has attempted to obtain a personal profit from any transaction in which the Employee
knows the Company has an interest, and which constitutes a corporate opportunity of the Company or
is adverse to the interests of the Company, unless the transaction was approved in writing by the
Company’s Chief Executive Officer after full disclosure of all details relating to such
transaction.

          (d) Termination Upon Death or Disability. Subject to Section 3.2, Employee’s employment and
the Company’s obligations under this Agreement shall terminate: (i) automatically, effective
immediately and without any notice being necessary, upon Employee’s death; or (ii) in the event of
the disability of Employee, by the Company giving notice of termination to Employee. For purposes
of this Agreement, “disability” means the inability of Employee, due to a physical or mental
impairment, for 180 days (whether or not consecutive) during any period of 360 days to perform,
with reasonable accommodation, the essential functions of the work contemplated by this Agreement.
In the event of any dispute as to whether Employee is disabled, the matter shall be determined by
the Company’s Chief Executive Officer in consultation with a physician satisfactory to the Company,
and Employee shall cooperate with the efforts to make such determination. Any such determination
shall be conclusive and binding on the parties. Any determination of disability under this Section 3.1(d)

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is not intended to alter any benefits any party may be entitled to receive under any
long-term disability insurance policy carried by either the Company or Employee with respect to
Employee, which benefits shall be governed solely by the terms of any such insurance policy.
Nothing in this subsection shall be construed as limiting or altering any of Employee’s rights
under state workers compensation laws or state or Federal family and medical leave laws.

          (e) Termination Upon Resignation or Retirement. Since Employee is an at-will
employee, subject to Section 3.2, Employee may terminate employment and all of the obligations
under this Agreement at any time and for any reason. If Employee terminates employment as a
result of retirement from the Company, Employee shall provide the Company with at least 90 days’
notice.

     3.2 Rights Upon Termination; Non-Renewal by Company.

          (a) Section 3.1(a) and 3.1(b) Termination. If Employee’s employment is terminated pursuant to
Section 3.1(a) or 3.1(b) hereof or upon expiration of this Agreement pursuant to the Company’s
notice of its intention not to renew pursuant to Section 1.1, Employee shall have no further rights
against the Company hereunder, except that the Company, subject to Section 3.2(g), will:

          (i) within 10 days following the termination of employment,
pay Employee (a) any unpaid Base Salary with respect to the period prior to
the effective date of termination, (b) reimbursement of expenses to which Employee
is entitled under Section 2.4 hereof, and payment of any accrued but unused vacation to
which Employee is entitled to under Section 2.5 hereof (collectively, the “Accrued Obligations.”).

          (ii) subject to Section 3.2(f), pay Employee a lump-sum severance payment (the
“Severance Payment”) 53 days following the Employee’s termination of employment, in an
amount equal to the sum of: (a) 12 months’ of Employee’s annual base salary as in effect on
the date of termination; and (b) the average of the two annual bonuses paid to Employee for
the two years immediately preceding the year in which such termination occurs; provided that
if the Employee was not employed for the period required to be eligible for two prior full
year annual bonuses, then the amount in this subparagraph (b) shall be the amount of the
annual bonus, if any, received for the year prior to the year in which termination of
employment occurred.

          (iii) subject to Section 3.2(f), pay the COBRA premium for group health care coverage
for Employee and Employee’s eligible dependents, as applicable and to the extent eligible,
provided that Employee properly elects COBRA continuation coverage, for up to twelve (12)
months immediately following the date of such termination of Employee’s employment, except
that payment of such premiums shall cease if and when the Employee (and Employee’s eligible
dependents) become eligible for medical, hospital and health coverage under a plan of a
subsequent employer; and

          (iv) subject to Section 3.2(f), pay up to $10,000 for outplacement services, such
services to be used within two years of termination of employment.

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          (b) Section 3.1(c) and 3.1(e) Termination. If Employee’s employment is terminated pursuant to
Sections 3.1(c) or 3.1(e) hereof, Employee shall have no further rights against the Company
hereunder, except for the right to receive the Accrued Obligations.

          (c) Section 3.1(d) Termination. If Employee’s employment is terminated pursuant to Section
3.1(d) hereof, Employee or Employee’s estate shall have no further rights against the Company
hereunder, except for the right to receive (i) the Accrued Obligations, (ii) payment of the COBRA
premium for group health care coverage for Employee and Employee’s eligible dependents, as
applicable and to the extent eligible, provided that Employee or Employee’s estate properly elects
COBRA continuation coverage, for up to twelve (12) months immediately following the date of such
termination of Employee’s employment, and (iii) the continuing rights under the life insurance
benefit under Section 2.3.

          (d) Termination Pursuant to a Change of Control. If, within three (3) months before or twenty
four (24) months following a Change of Control, the Company terminates Employee’s employment
without Cause pursuant to Section 3.1(a) or Employee terminates his employment for Good Reason
pursuant to Section 3.1(b), Employee shall have no further rights against the Company hereunder,
except the Company will, subject to Section 3.2(g):

          (i) pay the Employee the Accrued Obligations:

          (ii) subject to Section 3.2(f), pay Employee a lump-sum severance payment (the
“Severance Payment”) 53 days following the termination of employment, in an amount
equal to the sum of: (a) 2.0 times Employee’s annual base salary as in effect on the date
of termination; and (b) 2.0 times the greater of (x) the average of the two annual bonuses
paid to Employee for the two years preceding the year in which such termination occurs,
provided that if the Employee was not employed for the period required to be eligible for
two prior annual bonuses, then the amount in this subparagraph (b)(x) shall be the amount of
the annual bonus, if any, received for the year prior to the year in which termination of
employment occurred, or (y) the target bonus for the year in which such termination occurs;
provided such lump sum shall be reduced by the amount of any lump sum payable under Section
3.2(a)(ii).

          (iii) subject to Section 3.2(f), pay the COBRA premium for group health care
coverage for Employee and Employee’s eligible dependents, as applicable and to the extent
eligible, provided that Employee properly elects COBRA continuation coverage, for the 24
month period immediately following the date of such termination of Employee’s employment,
except that payment of such premiums shall cease if and when the Employee (and Employee’s
eligible dependents) become eligible for medical, hospital and health coverage under a plan
of a subsequent employer; and

          (iv) subject to Section 3.2(f), pay up to $10,000 for outplacement services, provided
such payment shall be reduced by the amount of any payment under Section 3.2(a)(iv), and
provided further that such services are used within two years of termination of employment.

          (e) Definition of Change of Control. As used herein, “Change of Control” shall mean
the occurrence of a “change in the ownership,” a “change in the effective control” or a “change in
the ownership of a substantial portion of the assets” of the Company, as determined

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in accordance
with this definition. In determining whether an event shall be considered a “change in the
ownership,” a “change in the effective control” or a “change in the ownership of a substantial
portion of the assets” of the Company, the following provisions shall apply:

     (i) A “change in the ownership” of the Company shall occur on the date on which any
one person, or more than one person acting as a group, acquires ownership of stock of the
Company that, together with stock held by such person or group, constitutes more than 50% of
the total fair market value or total voting power of the stock of the Company, as determined
in accordance with Treasury Regulation § 1.409A-3(i)(5)(v). If a person or group is
considered either to own more than 50% of the total fair market value or total voting power
of the stock of the Company, or to have effective control of the Company within the meaning
of part (b) of this definition, and such person or group acquires additional stock of the
Company, the acquisition of additional stock by such person or group shall not be considered
to cause a “change in the ownership” of the Company.

     (ii) A “change in the effective control” of the Company shall occur on either of
the following dates:

     (A) The date on which any one person, or more than one person acting as a
group, acquires (or has acquired during the 12-month period ending on the
date of the most recent acquisition by such person or persons) ownership of
stock of the Company possessing 30% or more of the total voting power of the stock
of the Company, as determined in accordance with Treasury Regulation §
1.409A-3(i)(5)(vi). If a person or group is considered to possess 30% or more of
the total voting power of the stock of the Company, and such person or group
acquires additional stock of the Company, the acquisition of additional stock by
such person or group shall not be considered to cause a “change in the effective
control” of the Company; or

     (B) The date on which a majority of the members of the Company’s Board of
Directors is replaced during any 12-month period by directors whose appointment or
election is not endorsed by a majority of the members of the Company’s Board of
Directors before the date of the appointment or election, as determined in
accordance with Treasury Regulation § 1.409A-3(i)(5)(vi).

     (iii) A “change in the ownership of a substantial portion of the assets” of the
Company shall occur on the date on which any one person, or more than one person acting as a
group, acquires (or has acquired during the 12-month period ending on the date of the most
recent acquisition by such person or persons) assets from the Company that have a total
gross fair market value equal to or more than 40% of the total gross fair market value of
all of the assets of the Company immediately before such acquisition or acquisitions, as
determined in accordance with Treasury Regulation § 1.409A-3(i)(5)(vii). A transfer of
assets shall not be treated as a “change in the ownership of a substantial portion of the
assets” when such transfer is made to an entity that is controlled by the shareholders of
the Company, as determined in accordance with Treasury Regulation § 1.409A-3(i)(5)(vii)(B).

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          (f) Exclusive Remedy; Waiver and Release. To the extent permitted by applicable law,
the payments contemplated by this Section 3.2 shall constitute the exclusive and sole remedy for
any termination of Employee’s employment by the Company (whether pursuant to, or in violation of,
the terms of this Agreement). Employee covenants not to assert or pursue any remedies, other than
an action to enforce the payments due to Employee under this Agreement, at law or in equity, with
respect to any termination of employment, and shall execute a release and waiver on such terms and
conditions as the Company may require as a condition of entitlement to such payments. If any
applicable revocation period for such release and waiver has not expired before the date payment is
due to be made hereunder, such payment shall be forfeited.

          (g) Limitation of Benefits. If any payments or benefits payable to the employee under
this Agreement or otherwise would be subject to the excise tax under Section 4999 of the Code, such
payments and/or benefits will be reduced to the extent necessary so that no amount will be subject
to such excise tax; provided that such reduction will only occur if the employee will be in a more
favorable, after-tax position than if no such reduction was made.

          (h) Six Month Delay. If payment of any amount of “deferred compensation” (as defined under Section 409A of the
Code, after giving effect to the exemptions thereunder) is triggered by a Separation from Service
(as defined in Section 4.7) that occurs while the Employee is a “specified employee” with respect
to the Company (as defined under Section 409A of the Code and determined in good faith), and if
such amount is scheduled to be paid within six (6) months after such Separation from Service, the
amount shall accrue without interest and shall be paid the first business day after the end of such
six-month period, or, if earlier, within 15 days after the appointment of the personal
representative or executor of the Employee’s estate following the Employee’s death.

ARTICLE IV

GENERAL PROVISIONS

     4.1 Notices. Any and all notices provided for in this Agreement shall be given in writing and
shall be deemed given to a party at the earlier of (i) when actually delivered to such party, or
(ii) when mailed to such party by registered or certified mail (return receipt requested) or sent
to such party by courier, confirmed by receipt, and addressed to such party at the address
designated below for such party as follows (or to such other address for such party as such party
may have substituted by notice pursuant to this Section 4.1):

	 	(a)	 	If to the Company:

TomoTherapy Incorporated

1240 Deming Way

Madison, WI 53717

Attn: General Counsel
	 
	 	(b)	 	If to Employee:

717 Oneida Place

Madison, WI 53711

Attn: Brenda S. Furlow

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     4.2 Entire Agreement. This Agreement contains the entire understanding and the full and
complete agreement of the parties and supersedes and replaces any prior understandings and
agreements among the parties, with respect to the subject matter hereof., provided that the
Indemnity Agreement dated November 5, 2008, the Confidentiality and Non-Competition Agreement
dated April 24, 2007, (“Confidentiality Agreement”) and the Assignment of Inventions Agreement
dated April 24, 2007, (“Assignment Agreement”) between the Company and the Employee are and shall
remain in effect. 

     4.3 Amendment. This Agreement may be altered, amended or modified only in a writing, signed by
both of the parties hereto. Headings included in this Agreement are for convenience only and are
not intended to limit or expand the rights of the parties hereto. References to Sections herein
shall mean sections of the text of this Agreement, unless otherwise indicated.

     4.4 Assignability. This Agreement and the rights and duties set forth herein may not be
assigned by Employee, but may be assigned by the Company, in whole or in part. This Agreement
shall be binding on and inure to the benefit of each party and such party’s respective heirs, legal
representatives, successors and assigns.

     4.5 Severability. If any court of competent jurisdiction determines that any provision of this
Agreement is invalid or unenforceable, then such invalidity or unenforceability shall have no
effect on the other provisions hereof, which shall remain valid, binding and enforceable and in
full force and effect, and such invalid or unenforceable provision shall be construed in a manner
so as to give the maximum valid and enforceable effect to the intent of the parties expressed
therein.

     4.6 Arbitration. Any controversy, dispute or claim arising out of or relating to this
Agreement (including, but not limited to, any claim regarding the scope or effect of this Section
and any claim that this Section is invalid or unenforceable), or the breach hereof, shall be
settled by a single arbitrator in binding arbitration conducted in Milwaukee, Wisconsin in
accordance with the Commercial Arbitration Rules of the American Arbitration Association (“AAA”)(or
such other arbitration service as the parties may agree upon), and judgment upon the award rendered
by the arbitrator may be entered in any court having jurisdiction thereof. The arbitrator’s
decision shall be in writing. In addition to the Commercial Arbitration Rules of the AAA and
unless otherwise agreed to by the parties, the following rules shall apply:

          (a) Each party shall be entitled to discovery exclusively by the following means: (i) requests
for admission, (ii) requests for production of documents, (iii) up to 15 written interrogatories
(with any subpart to be counted as a separate interrogatory), and (iv) depositions of no more than
six individuals.

          (b) Unless the arbitrator finds that delay is reasonably justified or as otherwise agreed to
by the parties, all discovery shall be completed, and the arbitration hearing shall commence within
five months after the appointment of the arbitrator.

          (c) Unless the arbitrator finds that delay is reasonably justified, the hearing will be
completed, and an award rendered within 30 days of commencement of the hearing.

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The arbitrator’s authority shall include the ability to render equitable types of relief and, in
such event, any aforesaid court may enter an order enjoining and/or compelling such actions or
relief ordered or as found by the arbitrator. The arbitrator also shall make a determination
regarding which party’s legal position in any such controversy or claim is the more substantially
correct (the “Prevailing Party”) and the arbitrator shall require the other party to pay the legal
and other professional fees and costs incurred by the Prevailing Party in connection with such
arbitration proceeding and any necessary court action. In addition, the parties expressly agree
that a court of competent jurisdiction may enter a temporary restraining order or an order
enjoining a breach of the Assignment Agreement, the Confidentiality Agreement or any similarly
subsequently executed agreement between the parties, pending a final award or further order by the
arbitrator.
Such remedy, however, shall be cumulative and nonexclusive, and shall be in addition to any other
remedy to which the parties may be entitled.

     4.7 Separation from Service. “Separation from Service,” “termination of employment,” or words
of similar import shall mean, with respect to any payments of deferred compensation subject to
Section 409A of the Code, the Employee’s “separation from service” as defined in Section 409A of
the Code. For this purpose, a “separation from service” is deemed to occur on the date that the
Company and the Employee reasonably anticipate that the level of bona fide services the Employee
would perform after the date (whether as an employee or independent contractor) would permanently
decrease to a level that, based on the facts and circumstances would constitute a separation from
service; provided that a decrease to a level that is 50% or more of the average level of bona fide
services provided over the prior 36 months shall not be a Separation from Service, and a decrease
to a level that is 20% or less of the average level of such bona fide services shall be a
Separation from Service. The bona fide services taken into account for purposes of determining
whether there has been a Separation from Service shall be services performed for the Company and
any person or entity that would be considered a single employer with the Company under Section
414(b) or 414(c) of the Code; provided that, in applying Section 1563(a)(1),(2), and (3) of the
Code, the language “at least 50 percent” shall be used instead of “at least 80 percent;” and
further provided that “at least 20 percent” shall be used instead of “at least 50 percent” where
based on legitimate business criteria.

     4.8 Waiver of Breach. The waiver by either party of the breach of any provision of this
Agreement shall not operate or be construed as a waiver of any subsequent breach by either party.

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     4.9 Governing Law; Construction. This Agreement shall be governed by the internal laws of the
State of Wisconsin, without regard to any rules of construction concerning the party responsible
for the drafting hereof.

     IN WITNESS WHEREOF, the parties have executed this Agreement as of the day and year written
above.

	 	 	 	 	 
	EMPLOYEE:

Brenda S. Furlow	COMPANY:

TomoTherapy Incorporated

 	 
	/s/ Brenda S. Furlow
	By:  	/s/ Frederick A. Robertson, M.D.
 	 
	 	 	Frederick A. Robertson, M.D. 	 
	 	 	Chief Executive Officer 	 
	 

10LOAN AGREEMENT WITH M&I MARSHALL & ILSLEY BANK

Exhibit 10.38

Confidential treatment has been requested for portions of this exhibit. The copy filed herewith
omits the information subject to the confidentiality request. Omissions are designated as [ * ].
A complete version of this exhibit has been filed separately with the Securities and Exchange
Commission.

M&I Marshall & Ilsley Bank

Loan Agreement (“Agreement”)

TomoTherapy Incorporated (“Borrower”) agrees with M&I Marshall & Ilsley Bank (“Bank”) to all terms
and conditions set forth in this Agreement so long as any obligation is owed Bank (“Loans”), or
Bank has any obligation to lend to the Borrower under any note evidencing a loan from the Borrower
to the Bank (the “Note”), and all extensions, renewals or modifications of any note evidencing a
loan.

	1)	 	CONDITIONS FOR LOANS. Bank’s obligation to make any loan is subject to satisfaction of the
following conditions:

	 	a)	 	Borrower shall not be in default under this Agreement or any other obligation to Bank
or to any other creditor of Borrower.

	2)	 	REPRESENTATIONS AND WARRANTIES. Borrower represents and warrants to Bank that on the date of
the Loans:

	 	a)	 	The Loans will be used solely for business purposes and are not and will not be used
for personal, family, household or agricultural purposes.
	 
	 	b)	 	Borrower will not use any part of the proceeds of the loans to purchase or carry any
margin stock within the meaning of Regulation U of the Board of Governors of the Federal
Reserve System.
	 
	 	c)	 	There is no litigation or administrative proceeding pending or, to the knowledge of
Borrower, threatened against Borrower, which might result in any material adverse change in
the business or financial condition of Borrower.
	 
	 	d)	 	Borrower has no notice or knowledge of any substance which has been, is, or will be
present, used, stored, deposited, treated, or disposed of on, under or about any real
estate now or at any time owned or occupied by the Borrower which would require clean up,
removal or some other remedial action under any federal, state or local laws, regulations,
ordinances, codes or rules. In the event any such substance is present on such real
estate, Borrower shall indemnify and hold harmless Bank, its directors, officers, employees
and agents from all loss, costs (including reasonable attorneys fees and expenses), and
liability of every kind and nature resulting from or arising out of or based upon such
substance. Borrower shall immediately notify bank in writing of any governmental or
regulatory action or third party claim instituted or threatened in connection with any such
substance.
	 
	 	e)	 	Borrower has paid all federal and state income taxes or other taxes of any kind owed by
it for all past years and no claim is being asserted against it with respect to any federal
or state income taxes for any past years or with respect to any other federal, state, or
other taxes of any kind or nature for any past years.

	3)	 	COVENANTS. Borrower shall, so long as any amounts remain unpaid:

	 	a)	 	Furnish to Bank, as soon as available, such financial information respecting Borrower
as Bank from time to time requests, and without request furnish to Bank:

	 	i)	 	Within one hundred twenty (120) days after the end of each fiscal year of
Borrower a balance sheet of Borrower as of the close of such fiscal year and related
statements of income and retained earnings for such year all in reasonable detail and
satisfactory in scope to Bank, audited by a certified public accounting firm acceptable
to Bank in accordance with generally accepted accounting principles applied on a
consistent basis, and
	 
	 	ii)	 	Within forty-five (45) days after the end of each quarter a balance sheet of
Borrower as of the end of such quarter and related statements of income and retained
earnings for the period from the beginning of the fiscal year to the end of such
quarter, prepared in accordance with generally accepted accounting principles applied on
a consistent basis, certified, subject to normal year-end adjustments, by the chief
financial representative of Borrower.

	 	b)	 	Keep complete and accurate business records. Permit any representative of the Bank to
visit and inspect any of the Borrower’s tangible or intangible properties as often as
desired by Bank.
	 
	 	c)	 	Permit Bank, at any reasonable time during business hours, access to all of the
financial records of Borrower to enable Bank to copy and/or audit Borrower’s financial
records using persons designated by Bank. Borrower shall pay Bank, upon demand, for the
reasonable cost of such audits.
	 
	 	d)	 	Not take any action or permit any event to occur which materially impairs Borrower’s
ability to make payments under this Agreement when due. Such events include, without
limitation, the fact that Borrower, or any surety or Guarantor for Borrower’s obligations
under this Agreement ceases to exist, dies, or becomes insolvent or the subject of
bankruptcy or insolvency proceedings.
	 
	 	e)	 	Maintain, preserve and keep its machinery, equipment and all other property in good
repair and condition and duly pay and discharge all taxes and other charges imposed upon
said properties.
	 
	 	f)	 	Timely perform and observe all of the following financial covenants, all calculated in
accordance with generally accepted principles of accounting applied on a consistent basis:

	 	i)	 	Maintain at all times a Tangible Net Worth (as defined below) of equal to or
greater than [ * ].
	 
	 	ii)	 	Maintain at all times a ratio of Total Liabilities to Tangible Net Worth equal to
or less than [ * ] to [ * ]. Calculated as: Total Liabilities/ Tangible Net Worth

Tangible Net Worth: shall mean the excess of the total of all assets of the Borrower and all
consolidated subsidiaries and affiliates, of every kind and character, other than goodwill,
corporate franchises and other intangibles, less the aggregate of all liabilities (excluding tax
asset value) and reserves of every kind and character of the Borrower and all consolidated
subsidiaries and affiliates, all determined in accordance with generally accepted principles of
accounting.

	 	g)	 	Not create or permit to exist any lien or encumbrance with respect to Borrower’s
property, except liens in favor of Bank, liens associated with existing loans provided to
Borrower by Wisconsin Department of Commerce and Madison Development Corporation, liens for
taxes if they are being contested in good faith by appropriate proceedings and for which
appropriate reserves are maintained and liens or encumbrances permitted under any of the
Security Documents.
	 
	 	h)	 	Borrower shall have a sixty (60) day right to cure period if any of the covenants are
not complied with.

	4)	 	ADDITIONAL SECURITY. Unless a lien would be prohibited by law or would render a nontaxable
account taxable, Borrower grants to Bank a security interest and lien in any deposit account
Borrower may at any time have with Bank to secure all debts, obligations and liabilities of
Borrower under this Agreement. Bank may at any time after the occurrence of an event of
default set-off any amount under this Agreement against any deposit balances or other money
now or hereafter owed to Borrower by Bank.

 

 

	5)	 	DEFAULT AND ACCELERATION. Any one or more of the following events shall constitute a default
hereunder and under the Notes:

	 	a)	 	Borrower fails to pay any amount when due under this Agreement or the Notes delivered
by Borrower pursuant to this Agreement;
	 
	 	b)	 	Any representation or warranty made under this Agreement or information provided by
Borrower in connection with this Agreement is or was false or fraudulent in any material
respect;
	 
	 	c)	 	Material adverse change occurs in Borrower’s financial condition;
	 
	 	d)	 	Borrower fails to timely observe or perform any of the covenants or duties contained in
this Agreement;
	 
	 	e)	 	Any guaranty of Borrower’s obligation under this Agreement is revoked or becomes
unenforceable for any reason;
	 
	 	f)	 	Any event of default occurs under any security agreement;
	 
	 	g)	 	A default by Borrower with respect to any terms or provisions of documents evidencing
any other indebtedness of Borrower to Bank;
	 
	 	h)	 	The Borrower shall admit in writing the inability to pay any of its debts or shall have
made a general assignment for the benefit of creditors, or shall have applied for or
otherwise have a receiver, trustee, or custodian appointed for any of its property or
assets;
	 
	 	i)	 	The occurrence of any other event which causes the Bank, in good faith, to deem itself
insecure;

Then, at Bank’s option, and upon verbal or written notice to Borrower, given at any time including
after receipt from Borrower of a request for a Loan, Bank’s obligation to make Loans under this
Agreement shall terminate and the total unpaid balance shall become immediately due and payable
without presentment, demand, protest or further notice of any kind, all of which are hereby
expressly waived by Borrower.

Bank’s obligation to make Loans under this Agreement shall automatically terminate and the total
unpaid balance of the Notes shall automatically become due and payable in the event Borrower
becomes the subject of bankruptcy or other insolvency proceedings. Bank may waive any default
without waiving any other subsequent or prior default. Borrower agrees to pay Bank’s cost of
administration of this Agreement, including reasonable attorneys’ fees. Borrower also agrees to
pay all of Bank’s costs of collection, before and after judgment, including reasonable attorneys’
fees.

	6)	 	CROSS DEFAULT OF ALL OTHER OBLIGATIONS OF BORROWER WITH BANK. As an inducement to Bank to
extend the credit referenced herein, Borrower agrees that in the event it is in default with
respect to this Agreement, or the Notes delivered pursuant hereto, it shall also be in default
with respect to all other agreements, notes, or other documents evidencing Borrower’s other
indebtedness to Bank. Conversely, if any payment is not made when due under any other note,
agreement, assignment or mortgage in favor of the Bank, or if any event of default should
occur as defined in any such note, agreement, assignment or mortgage, the unpaid balance of
the Notes shall at the option of the holder and without notice, mature and become immediately
due and payable.

	7)	 	TERMINATION. Unless sooner terminated by Borrower’s default, Borrower’s right to obtain
loans and Bank’s obligation to extend the credit under this Agreement shall terminate on the
date the Notes are due by maturity or default (the “Termination Date”). The Borrower may
terminate Borrower’s right to obtain loans under this Agreement at any time and for any reason
by written notice to Bank. Such notice of termination signed by Borrower shall be binding on
each Borrower who signs this Agreement. Termination, for whatever reason, does not affect
Bank’s rights, powers and privileges, nor Borrower’s duties and liabilities, with regard to
the then-existing balance under this Agreement.

	8)	 	ENTIRE AGREEMENT. This Agreement is intended by Borrower and Bank as a final expression of
this Agreement and as a complete and exclusive statement of its terms, there being no
conditions to the full effectiveness of this Agreement except as set forth in this Agreement.
	 
	9)	 	NO WAIVER; REMEDIES. No failure on the part of Bank to exercise, and no delay in exercising,
any right, power or remedy under this Agreement shall operate as a waiver of such right, power
or remedy; nor shall any single or partial exercise of any right under this Agreement preclude
any other or further exercise of the right or the exercise of any other right. The remedies
provided in this Agreement are cumulative and not exclusive of any remedies provided by law.
	 
	10)	 	ISDA. Obligations and Indebtedness includes, without limitation all obligations,
indebtedness and liabilities arising pursuant to or in connection with any interest rate swap
transaction, basis swap, forward rate transaction, interest rate option, price risk hedging
transaction or any similar transaction between the Borrower and Bank.
	 
	11)	 	INTERPRETATION. The validity, construction and enforcement of this Agreement are governed by
the internal laws of Wisconsin. Invalidity of any provision of this Agreement shall not
affect the validity of any other provisions of this Agreement.
	 
	12)	 	CONFLICT BETWEEN THIS AGREEMENT AND THE NOTES. In the case of any ambiguity or conflict
between this Agreement and the Notes, this Agreement will govern.
	 
	13)	 	PREVIOUS LOAN AGREEMENTS. This Agreement supersedes and replaces all previous loan
agreements between Bank and Borrower.

     Dated as of December 1, 2007

	 	 	 	 	 	 	 	 	 	 	 
	TomoTherapy Incorporated	 	 	 	M&I Marshall & Ilsley Bank	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Frederick A. Robertson, MD
 

	 	 	 	By:
	 	/s/ Kirt C. Soukup
 

	 	 
	Frederick A. Robertson, MD, Chief Executive Officer	 	 	 	Kirt C. Soukup, Vice President	 	 

	 	 	 	 	 	 	 	 	 	 	 
	Drafted By: br	 	 	 
	Loan [ * ]	 	 	 	By:
	 	/s/ Jeff Ticknor 

	 	 
	 	 	 	Jeff Ticknor, Senior Vice President

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