Document:

EX-10.4

Exhibit 10.4

Assumption Agreement and First Amendment

to

Loan And Security Agreement

THIS ASSUMPTION AGREEMENT AND FIRST AMENDMENT to Loan and Security Agreement (this “Amendment”) is
entered into as of February 25, 2009, by and between SILICON VALLEY BANK (“Bank”), CARDIOVASCULAR
SYSTEMS, INC. (formerly known as Replidyne, Inc.), a Delaware corporation, for itself and as
successor to Existing Borrower (“Successor Borrower”), whose address is 651 Campus Drive, Saint
Paul, MN 55112, and CSI MINNESOTA, INC. (formerly known as Cardiovascular Systems, Inc.), a
Minnesota corporation (“Existing Borrower”), whose address is 651 Campus Drive, Saint Paul, MN
55112. (Successor Borrower and Existing Borrower are referred to herein, jointly and severally, as
“Borrower”.)

Recitals

     A. Bank and Existing Borrower have entered into that certain Loan and Security Agreement dated
September 12, 2008 (as the same may from time to time be amended, modified, supplemented or
restated in writing, the “Loan Agreement”).

     B. Bank has extended credit to Existing Borrower for the purposes permitted in the Loan
Agreement.

     C. Existing Borrower and Successor Borrower have advised Bank that Existing Borrower shall
merge into Successor Borrower, with Successor Borrower being the surviving corporation (the
“Merger”).

     D. Existing Borrower and Successor Borrower have requested that the Loan Agreement and other
Loan Documents be amended and supplemented in order to allow Successor Borrower to become the
borrower under the Loan Agreement and other Loan Documents.

     E. Bank has agreed to so amend and supplement the Loan Agreement and other Loan Documents, but
only to the extent, in accordance with the terms, subject to the conditions and in reliance upon
the representations, warranties and agreements set forth below.

Agreement

     Now, Therefore, in consideration of the foregoing recitals and other good and
valuable consideration, the receipt and adequacy of which is hereby acknowledged, and intending to
be legally bound, the parties hereto agree as follows:

1. Definitions. Capitalized terms used but not defined in this Amendment shall have the meanings
given to them in the Loan Agreement.

 

 

2. Assumption. Effective immediately upon the Merger, Successor Borrower, without any further
action, hereby assumes and agrees to perform for the benefit of Bank all of the “Obligations” (as
defined in the Loan Agreement) of Existing Borrower, and Successor Borrower agrees to honor,
perform and in all respects comply with all terms and provisions of all of the Loan Documents
(including, without limitation, the Loan Agreement and the Term Loan B Promissory Notes) to the
same extent as though Successor Borrower were named therein jointly and severally with Existing
Borrower. Effective immediately upon the Merger, all references in the Loan Agreement to
“Collateral” and “Obligations” shall be deemed to refer to all present and future Collateral and
Obligations (as therein defined) of Successor Borrower as well as Existing Borrower, and all
references in the Loan Documents to “Borrower” shall be deemed to refer to Successor Borrower for
itself and as successor to Existing Borrower. For example and without limitation on the generality
of the foregoing, (i) the term “Loan Documents” as defined in the Loan Agreement shall include
agreements executed by Existing Borrower prior to the Merger as well as agreements executed by
Successor Borrower, and (ii) Section 5.11 of the Loan Agreement which reads as follows:

No written representation, warranty or other statement of Borrower
in any certificate or written statement given to Bank, as of the
date such representation, warranty, or other statement was made,
taken together with all such written certificates and written
statements given to Bank, contains any untrue statement of a
material fact or omits to state a material fact necessary to make
the statements contained in the certificates or statements not
misleading (it being recognized by Bank that the projections and
forecasts provided by Borrower in good faith and based upon
reasonable assumptions are not viewed as facts and that actual
results during the period or periods covered by such projections
and forecasts may differ from the projected or forecasted
results).

shall apply to such representations, warranties or other statements whether given by Successor
Borrower upon or after the Merger or by Existing Borrower or Cardiovascular Systems, Inc. (fka
Replidyne, Inc.) prior to the Merger.

3. No Offset or Counterclaim. Existing Borrower and Successor Borrower acknowledge that the
Obligations are owing to Bank from Existing Borrower and, effective immediately upon the Merger,
will be owing from Successor Borrower, without any defense, offset or counterclaim of any kind or
nature whatsoever.

4. Grant of Security Interest. Without limiting the generality of the provisions of Section 2
above, effective immediately upon the Merger, as security for all Obligations, Successor Borrower
grants to Bank a continuing security interest in, and pledges to Bank, all of the following,
whether now owned or hereafter acquired, and wherever located: All of the “Collateral” (as defined
in the Loan Agreement) of Successor Borrower. Effective

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immediately upon the Merger, all references in the Loan Agreement to Collateral shall be deemed to
refer to the Collateral of each of Existing Borrower and Successor Borrower.

5. Merger Consent. Reference is made to the Consent Regarding RMS Merger, dated February 25, 2009,
entered into between Bank and Existing Borrower. Borrowers hereby confirm and agree to perform the
covenants and conditions agreed to by Existing Borrower pursuant to such Consent.

6. Financial and Merger-Related Representations and Warranties. Borrowers represent and warrant
that the financial statements and reports of Cardiovascular Systems, Inc. (fka Replidyne, Inc.)
delivered to Bank and/or filed with the Securities and Exchange Commission fairly present in all
material respects the financial condition and results of operations of Cardiovascular Systems, Inc.
(fka Replidyne, Inc.). Borrowers represent and warrant that there has not been any deterioration
in the financial condition of Cardiovascular Systems, Inc. (fka Replidyne, Inc.) that is not
reflected in such financial statements and reports. Borrowers represent and warrant that they have
delivered to Bank true and complete copies of the Agreement and Plan of Merger and Reorganization
dated November 3, 2008, among Responder Merger Sub, Inc. (“Merger Sub”), Successor Borrower and
Existing Borrower (the “Merger Agreement”), the “Company Disclosure Schedule” (as defined in the
Merger Agreement), and the “Replidyne Disclosure Schedule” (as defined in the Merger Agreement),
and all amendments, supplements and updates thereto. The representations and warranties of Merger
Sub, Successor Borrower and Existing Borrower contained in the Merger Agreement, Company Disclosure
Schedule, and Replidyne Disclosure Schedule, shall be deemed made to Bank and shall survive the
“Effective Date” as defined in the Merger Agreement, and continue in favor of Bank, notwithstanding
Section 10.1 of the Merger Agreement, or anything else to the contrary.

7. Modifications and Clarifications Regarding Loan Documents.

     7.1 Delay in Availability. Notwithstanding Section 2.1.1(a) of the Loan Agreement or any
other provision of the Loan Documents, Bank shall have no obligation to make any Advances or allow
the use of the Revolving Line for Cash Management Services (except for Cash Management Services of
up to $200,000 for business credit card purposes), until Bank has received a search from the
Delaware Secretary of State confirming the filing and priority of Bank’s UCC financing statement
against Successor Borrower.

     7.2 Insurance. To the extent that Section 6.7 of the Loan Agreement requires any advance
notice to Bank of Borrower’s insurance being changed to recognize the change of identity from
Existing Borrower to Successor Borrower, such advance notice is hereby waived.

     7.3 Collateral Accounts. Reference is made to Section 6.8(a) of the Loan Agreement which
reads as follows:

(a) Maintain all of its and all of its Subsidiaries’ operating and other
deposit accounts, securities accounts, and any other

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accounts at which Borrower or its Subsidiaries maintain funds or
investments (including without limitation any Collateral Accounts, but
excluding the Auction Rate Securities (UBS)) with Bank and Bank’s
Affiliates.

Notwithstanding anything to the contrary in Section 6.8 of the Loan Agreement, Successor
Borrower shall have until 30 days following the date of the Merger to close any of its
accounts that are not allowed to be maintained other than with Bank and Bank’s Affiliates
in accordance with Section 6.8(a) of the Loan Agreement, and during such period Borrower
shall not be required to provide Control Agreements with respect to such accounts.

     7.4 Changes in Ownership. Section 7.2(c) of the Loan Agreement reads as follows:

(c) permit a change in the record or beneficial ownership of an aggregate
of more than 20% of the outstanding shares of stock of Borrower, in one or
more transactions, compared to the ownership of outstanding shares of
stock of Borrower in effect on the date hereof (other than by the sale of
Borrower’s equity securities in a public offering or to private equity
investors so long as Borrower identifies to Bank the private equity
investors prior to the closing of the transaction); or

Effective immediately upon the Merger, said Section 7.2(c) is hereby amended to read as follows:

(c) permit or suffer any Change in Control; or

     7.5 Assumption Agreement. The following definition is hereby added to Section 13.1 of the
Loan Agreement in the appropriate alphabetical order:

“Assumption Agreement” is that certain Assumption Agreement and First
Amendment to Loan and Security Agreement, dated February 25, 2009, among
Bank, Cardiovascular Systems, Inc. (fka Replidyne, Inc.), and CSI
Minnesota (fka Cardiovascular Systems, Inc.).

     7.6 Change in Control. The following definition is hereby added to Section 13.1 of the Loan
Agreement in the appropriate alphabetical order:

“Change in Control” means any event, transaction, or occurrence as a
result of which any “person” (as such term is defined in Sections 3(a)(9)
and 13(d)(3) of the Securities Exchange Act of 1934, as an amended (the
“Exchange Act”)), other than a trustee or other fiduciary holding
securities under an employee benefit plan of Borrower, is or becomes a
beneficial owner (within the meaning Rule 13d-3 promulgated under the
Exchange Act), directly or indirectly, of securities of Borrower,
representing

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twenty percent (20%) or more of the combined voting power of Borrower’s
then outstanding securities.

     7.7 Designated Deposit Account. The definition of “Designated Deposit Account” contained in
Section 13.1 of the Loan Agreement reads as follows:

“Designated Deposit Account” is Borrower’s deposit account, account number
                       ,
maintained with Bank.

Borrower and Bank acknowledge and agree that, following the Merger, Bank intends to have a
new Designated Deposit Account opened with respect to Successor Borrower because Existing
Borrower, for which the above-referenced Designated Deposit Account was opened, will have
merged into Successor Borrower. Borrower will cooperate with the opening of such new
Designated Deposit Account.

     7.8 Initial Projections. For purposes of clarity, Bank and Borrower acknowledge and agree that
the “Initial Projections” as defined in Section 13.1 of the Loan Agreement shall continue to be the
projections provided by Existing Borrower for purposes of entering into the Loan Agreement.

     7.9 Perfection Certificate. The definition of “Perfection Certificate” contained in Section
13.1 of the Loan Agreement reads as follows:

“Perfection Certificate” is defined in Section 5.1.

Effective immediately upon the Merger, said definition is amended to read as
follows:

“Perfection Certificate” is defined in Section 5.1 provided that
“Perfection Certificate” shall, (a) with reference to “Existing
Borrower” (as defined in the Assumption Agreement) prior to the
Merger, mean the Perfection Certificate delivered by Existing
Borrower, dated September 12, 2008, (b) with reference to
“Successor Borrower” (as defined in the Assumption Agreement)
prior to the Merger, mean the pre-Merger Perfection Certificate
delivered by Successor Borrower, dated February 25, 2009, and (c)
with reference to the “Borrower” (as defined in the Assumption
Agreement) upon and after the Merger, mean the post-Merger
Perfection Certificate delivered by Successor Borrower, dated
February 25, 2009.

8. Limitation of Amendments.

     8.1 The consents and amendments set forth in this Amendment are effective for the purposes set
forth herein and shall be limited precisely as written and shall not be deemed to (a) be a consent
to any amendment, waiver or modification of any other term

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or condition of any Loan Document, or (b) otherwise prejudice any right or remedy which Bank
may now have or may have in the future under or in connection with any Loan Document.

     8.2 This Amendment shall be construed in connection with and as part of the Loan Documents and
all terms, conditions, representations, warranties, covenants and agreements set forth in the Loan
Documents, except as herein amended, are hereby ratified and confirmed and shall remain in full
force and effect.

9. Representations and Warranties. To induce Bank to enter into this Amendment, Borrower hereby
represents, warrants and agrees as follows:

     9.1 Immediately after giving effect to this Amendment and immediately after giving effect to
the Merger (a) the representations and warranties contained in the Loan Documents are true,
accurate and complete in all material respects as of the date hereof and as of the date of the
Merger (except to the extent such representations and warranties relate to an earlier date, in
which case they are true and correct in all material respects as of such date), and (b) no Event of
Default has occurred and is continuing;

     9.2 Borrower has the power and authority to execute and deliver this Amendment and to perform
its obligations under the Loan Agreement, as amended by this Amendment;

     9.3 The organizational documents of Successor Borrower previously delivered to Bank (including
the amendment referenced in the Merger Consent) remain true, accurate and complete and have not
been amended, supplemented or restated and are and continue to be in full force and effect;

     9.4 The execution and delivery by Borrower of this Amendment and the performance by Borrower
of its obligations under the Loan Agreement, as amended by this Amendment, have been duly
authorized;

     9.5 The execution and delivery by Borrower of this Amendment and the performance by Borrower
of its obligations under the Loan Agreement, as amended by this Amendment, do not and will not
contravene (a) any law or regulation binding on or affecting Borrower, (b) any contractual
restriction with a Person binding on Borrower, (c) any order, judgment or decree of any court or
other governmental or public body or authority, or subdivision thereof, binding on Borrower, or (d)
the organizational documents of Borrower;

     9.6 The execution and delivery by Borrower of this Amendment and the performance by Borrower
of its obligations under the Loan Agreement, as amended by this Amendment, do not require any
order, consent, approval, license, authorization or validation of, or filing, recording or
registration with, or exemption by any governmental or public body or authority, or subdivision
thereof, binding on either Borrower, except as already has been obtained or made; and

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     9.7 This Amendment has been duly executed and delivered by Borrower and is the binding
obligation of Borrower, enforceable against Borrower in accordance with its terms, except as such
enforceability may be limited by bankruptcy, insolvency, reorganization, liquidation, moratorium or
other similar laws of general application and equitable principles relating to or affecting
creditors’ rights.

10. Expenses. Without limitation on the terms of the Loan Documents, Borrower agrees to reimburse
Bank for all its reasonable costs and expenses (including reasonable attorneys’ fees) incurred in
connection with this Amendment. Bank is authorized to charge said fees, costs and expenses to
Borrower’s loan account or any of Borrower’s deposit accounts maintained with Bank.

11. Counterparts. This Amendment may be executed in any number of counterparts and all of such
counterparts taken together shall be deemed to constitute one and the same instrument.

[Signature Page Follows]

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     In Witness Whereof, the parties hereto have caused this Amendment to be duly executed
and delivered as of the date first written above.

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	SILICON VALLEY BANK	 	 	 	CARDIOVASCULAR SYSTEMS, INC.	 	 
	 	 	 	 	 	 	 	 	(fka Replidyne, Inc.)	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	By:	 	/s/ Benjaman Johnson	 	 	 	By:	 	/s/ Laurence L. Betterley	 	 
	 	 	 	 	 	 	 	 	 	 	 
	 

	 	Name:
	 	Benjaman Johnson
	 	 	 	 	 	Name
	 	Laurence L. Betterly	 	 
	 

	 	Title:
	 	Deal Team Leader
	 	 	 	 	 	Title:
	 	Chief Financial Officer	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	CSI MINNESOTA, INC.	 	 
	 	 	 	 	 	 	 	 	(fka Cardiovascular Systems, Inc.)	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	By:	 	/s/ David L. Martin	 	 
	 	 	 	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	 	 	Name:
	 	David L. Martin	 	 
	 

	 	 	 	 	 	 	 	 	 	Title:
	 	Chief Executive Officer	 	 

8EX-10.5

Exhibit 10.5

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF
1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AND PURSUANT TO THE
PROVISIONS OF ARTICLE 5 BELOW, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR
HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND APPLICABLE STATE SECURITIES LAW OR, IN
THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES,
SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION.

AMENDED AND RESTATED

WARRANT TO PURCHASE STOCK

	 	 	 
	Company:
	 	Cardiovascular Systems, Inc., a Delaware
Corporation (formerly known as Replidyne, Inc.)
	Number of Shares:
	 	8,493
	Class of Stock:
	 	Common Stock
	Warrant Price:
	 	$14.16 per share
	Restated Warrant Date
	 	February 25, 2009
	Issue Date:
	 	September 12, 2008
	Expiration Date:
	 	The 10th anniversary after the Issue Date
	Credit Facility:
	 	This Warrant is issued in connection with the Term
Loan A referenced in the Loan and Security Agreement
dated September 12, 2008 between Silicon Valley Bank
and Company (as successor by merger to
Cardiovascular Systems, Inc., a Minnesota
corporation.)

     Reference is made to the Warrant to Purchase Stock (the “Pre-Amendment Warrant”), with an
Issue Date of September 12, 2008, by Cardiovascular Systems, Inc., a Minnesota corporation
(“Original Issuer”), in favor of Silicon Valley Bank, and assigned by Silicon Valley Bank to SVB
Financial Group. The Original Issuer has merged with a wholly-owned subsidiary of Company and, as
a result of such merger and in accordance with Section 1.6.2(C) of the Pre-Amendment Warrant,
Company has assumed the obligations of the Pre-Amendment Warrant as hereby amended and restated.
This Warrant amends and restates the Pre-Amendment Warrant.

     THIS WARRANT CERTIFIES THAT, for good and valuable consideration, SVB FINANCIAL GROUP (SVB
Financial Group, together with any registered holder from time to time of this Warrant or any
holder of the shares issuable or issued upon exercise of this Warrant, “Holder”) is entitled to
purchase the number of fully paid and nonassessable shares of the class of securities (the
“Shares”) of the Company at the Warrant Price, all as set forth above and as adjusted pursuant to
Article 2 of this Warrant, subject to the provisions and upon the terms and conditions set forth in
this Warrant.

ARTICLE 1. EXERCISE.

          1.1 Method of Exercise. Holder may exercise this Warrant by delivering a duly
executed Notice of Exercise in substantially the form attached as

 

 

Appendix 1 to the principal office of the Company. Unless Holder is exercising the conversion
right set forth in Article 1.2, Holder shall also deliver to the Company a check, wire transfer (to
an account designated by the Company), or other form of payment acceptable to the Company for the
aggregate Warrant Price for the Shares being purchased.

          1.2 Conversion Right. In lieu of exercising this Warrant as specified in Article 1.1,
Holder may from time to time convert this Warrant, in whole or in part, into a number of Shares
determined by dividing (a) the aggregate fair market value of the Shares or other securities
otherwise issuable upon exercise of this Warrant minus the aggregate Warrant Price of such Shares
by (b) the fair market value of one Share. The fair market value of the Shares shall be determined
pursuant to Article 1.3.

          1.3 Fair Market Value. If the Company’s common stock is traded in a public market and
the Shares are common stock, the fair market value of each Share shall be the closing price of a
Share reported for the business day immediately before Holder delivers its Notice of Exercise to
the Company (or in the instance where the Warrant is exercised immediately prior to the
effectiveness of the Company’s initial public offering, the “price to public” per share price
specified in the final prospectus relating to such offering). If the Company’s common stock is
traded in a public market and the Shares are preferred stock, the fair market value of a Share
shall be the closing price of a share of the Company’s common stock reported for the business day
immediately before Holder delivers its Notice of Exercise to the Company (or, in the instance where
the Warrant is exercised immediately prior to the effectiveness of the Company’s initial public
offering, the initial “price to public” per share price specified in the final prospectus relating
to such offering), in both cases, multiplied by the number of shares of the Company’s common stock
into which a Share is convertible in accordance with the Company’s Articles of Incorporation. If
the Company’s common stock is not traded in a public market, the Board of Directors of the Company
shall determine fair market value in its reasonable good faith judgment.

          1.4 Delivery of Certificate and New Warrant. Promptly after Holder exercises or
converts this Warrant and, if applicable, the Company receives payment of the aggregate Warrant
Price, the Company shall deliver to Holder certificates for the Shares acquired and, if this
Warrant has not been fully exercised or converted and has not expired, a new Warrant representing
the Shares not so acquired.

          1.5 Replacement of Warrants. On receipt of evidence reasonably satisfactory to the
Company of the loss, theft, destruction or mutilation of this Warrant and, in the case of loss,
theft or destruction, on delivery of an indemnity agreement reasonably satisfactory in form and
amount to the Company or, in the case of mutilation on surrender and cancellation of this Warrant,
the Company shall execute and deliver, in lieu of this Warrant, a new warrant of like tenor.

          1.6 Treatment of Warrant Upon Acquisition of Company.

               1.6.1 “Acquisition”. For the purpose of this Warrant, “Acquisition” means any sale,
license, or other disposition of all or substantially all of the assets of the Company, or any
reorganization, consolidation, or merger of the Company where the holders of the Company’s
securities before the transaction beneficially own

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less than 50% of the outstanding voting securities of the surviving entity after the transaction.

               1.6.2 Treatment of Warrant at Acquisition.

A) Upon the written request of the Company, Holder agrees that, in the event of an Acquisition that
is not an asset sale and in which the sole consideration is cash, either (a) Holder shall exercise
its conversion or purchase right under this Warrant and such exercise will be deemed effective
immediately prior to the consummation of such Acquisition or (b) if Holder elects not to exercise
the Warrant, this Warrant will expire upon the consummation of such Acquisition. The Company shall
provide Holder with written notice of its request relating to the foregoing (together with such
reasonable information as Holder may request in connection with such contemplated Acquisition
giving rise to such notice), which is to be delivered to Holder not less than ten (10) days prior
to the closing of the proposed Acquisition.

B) Upon the written request of the Company, Holder agrees that, in the event of an Acquisition that
is an “arms length” sale of all or substantially all of the Company’s assets (and only its assets)
to a third party that is not an Affiliate (as defined below) of the Company (a “True Asset Sale”),
either (a) Holder shall exercise its conversion or purchase right under this Warrant and such
exercise will be deemed effective immediately prior to the consummation of such Acquisition or (b)
if Holder elects not to exercise the Warrant, this Warrant will continue until the Expiration Date
if the Company continues as a going concern following the closing of any such True Asset Sale. The
Company shall provide Holder with written notice of its request relating to the foregoing (together
with such reasonable information as Holder may request in connection with such contemplated
Acquisition giving rise to such notice), which is to be delivered to Holder not less than ten (10)
days prior to the closing of the proposed Acquisition.

C) Upon the closing of any Acquisition other than those particularly described in subsections (A)
and (B) above, the successor entity shall assume the obligations of this Warrant, and this Warrant
shall be exercisable for the same securities, cash, and property as would be payable for the Shares
issuable upon exercise of the unexercised portion of this Warrant as if such Shares were
outstanding on the record date for the Acquisition and subsequent closing. The Warrant Price
and/or number of Shares shall be adjusted accordingly.

As used herein “Affiliate” shall mean any person or entity that owns or controls directly
or indirectly ten (10) percent or more of the stock of Company, any person or entity that controls
or is controlled by or is under common control with such persons or entities, and each of such
person’s or entity’s officers, directors, joint venturers or partners, as applicable.

ARTICLE 2. ADJUSTMENTS TO THE SHARES.

          2.1 Stock Dividends, Splits, Etc. If the Company declares or pays a dividend on the
Shares payable in common stock, or other securities, then upon exercise of this Warrant, for each
Share acquired, Holder shall receive, without cost to Holder, the total number and kind of
securities to which Holder would have been entitled had Holder owned the Shares of record as of the
date the dividend occurred. If the Company subdivides the Shares by reclassification or otherwise
into a greater number of

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shares or takes any other action which increase the amount of stock into which the Shares are
convertible, the number of shares purchasable hereunder shall be proportionately increased and the
Warrant Price shall be proportionately decreased. If the outstanding shares are combined or
consolidated, by reclassification or otherwise, into a lesser number of shares, the Warrant Price
shall be proportionately increased and the number of Shares shall be proportionately decreased.

          2.2 Reclassification, Exchange, Combinations or Substitution. Upon any
reclassification, exchange, substitution, or other event that results in a change of the number
and/or class of the securities issuable upon exercise or conversion of this Warrant, Holder shall
be entitled to receive, upon exercise or conversion of this Warrant, the number and kind of
securities and property that Holder would have received for the Shares if this Warrant had been
exercised immediately before such reclassification, exchange, substitution, or other event. Such
an event shall include any automatic conversion of the outstanding or issuable securities of the
Company of the same class or series as the Shares to common stock pursuant to the terms of the
Company’s Articles or Certificate (as applicable) of Incorporation upon the closing of a registered
public offering of the Company’s common stock or other conversion in accordance with the Company’s
Articles of Incorporation. The Company or its successor shall promptly issue to Holder an
amendment to this Warrant setting forth the number and kind of such new securities or other
property issuable upon exercise or conversion of this Warrant as a result of such reclassification,
exchange, substitution or other event that results in a change of the number and/or class of
securities issuable upon exercise or conversion of this Warrant. The amendment to this Warrant
shall provide for adjustments which shall be as nearly equivalent as may be practicable to the
adjustments provided for in this Article 2 including, without limitation, adjustments to the
Warrant Price and to the number of securities or property issuable upon exercise of the new
Warrant. The provisions of this Article 2.2 shall similarly apply to successive reclassifications,
exchanges, substitutions, or other events.

          2.3 Adjustments for Diluting Issuances. The Warrant Price and the number of Shares
issuable upon exercise of this Warrant or, if the Shares are preferred stock, the number of shares
of common stock issuable upon conversion of the Shares, shall be subject to adjustment, from time
to time in the manner set forth in the Company’s Articles or Certificate of Incorporation as if
the Shares were issued and outstanding on and as of the date of any such required adjustment. The
provisions set forth for the Shares in the Company’s Articles or Certificate (as applicable) of
Incorporation relating to the above in effect as of the Restated Warrant Date may not be amended,
modified or waived, without the prior written consent of Holder unless such amendment,
modification or waiver affects the rights associated with the Shares in the same manner as such
amendment, modification or waiver affects the rights associated with all other shares of the same
series and class as the Shares granted to Holder.

          2.4 No Impairment. The Company shall not, by amendment of its Articles or Certificate
(as applicable) of Incorporation or through a reorganization, transfer of assets, consolidation,
merger, dissolution, issue, or sale of securities or any other voluntary action, seek to avoid the
observance or performance of any of the terms to be observed or performed under this Warrant by the
Company, and shall at all times in good faith assist in carrying out of all the provisions of this
Article 2 and in taking all such action as may be necessary or appropriate to protect Holder’s
rights under this Article against impairment.

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          2.5 Fractional Shares. No fractional Shares shall be issuable upon exercise or
conversion of this Warrant and the number of Shares to be issued shall be rounded down to the
nearest whole Share. If a fractional share interest arises upon any exercise or conversion of the
Warrant, the Company shall eliminate such fractional share interest by paying Holder the amount
computed by multiplying the fractional interest by the fair market value of a full Share.

          2.6 Certificate as to Adjustments. Upon each adjustment of the Warrant Price, the
Company shall promptly notify Holder in writing, and, at the Company’s expense, promptly compute
such adjustment, and furnish Holder with a certificate of its Chief Financial Officer setting forth
such adjustment and the facts upon which such adjustment is based. The Company shall, upon written
request, furnish Holder a certificate setting forth the Warrant Price in effect upon the date
thereof and the series of adjustments leading to such Warrant Price.

ARTICLE 3. REPRESENTATIONS AND COVENANTS OF THE COMPANY.

          3.1 Representations and Warranties. The Company represents and warrants to Holder as
follows:

               (a) The representations and warranties made by Original Issuer in Section 3.1 of the
Pre-Amendment Warrant shall survive this amendment and restatement of the Pre-Amendment Warrant.

               (b) All Shares which may be issued upon the exercise of the purchase right represented by this
Warrant, and all securities, if any, issuable upon conversion of the Shares, shall, upon issuance,
be duly authorized, validly issued, fully paid and nonassessable, and free of any liens and
encumbrances except for restrictions on transfer provided for herein or under applicable federal
and state securities laws.

               (c) The Company’s capitalization table attached hereto as Schedule 1 is true and
complete as of the Restated Warrant Date.

               (d) The Company’s issuance of this Warrant will not trigger any adjustment to the conversion
prices of the Company’s preferred stock pursuant to the Company’s Articles of Incorporation.

          3.2 Notice of Certain Events. If at any time the Company shall plan (a) the
declaration of any dividend upon its common stock payable in cash or stock or any other
distribution to the holders of its common stock; (b) to offer for sale any shares of the Company’s
capital stock (or other securities convertible into such capital stock), other than (i) pursuant to
the Company’s stock option or other compensatory plans, (ii) in connection with commercial credit
arrangements or equipment financings, or (iii) in connection with strategic transactions for
purposes other than capital raising; (c) any capital reorganization or reclassification of the
capital stock of the Company, or a consolidation or merger of the Company with or into, or a sale,
lease, license, or other conveyance of all or substantially all its assets to, another entity or
entities; (e) a voluntary or involuntary dissolution, liquidation or winding up of the Company; or
(f) offer holders of registration rights the opportunity to participate in an underwritten public
offering of the Company’s securities for cash; then, in any one or more of said cases, the

5

 

Company shall give Holder: (1) at least 20 days’ prior written notice of the date on which the
books of the Company shall close or a record shall be taken for such dividend, distribution or
subscription rights or for determining rights to vote in respect of any of the matters referred to
in (a) through (e) above, and (2) in the case of any of the matters referred to in (c) through (e)
above, at least 20 days’ prior written notice of the date when the same shall take place, and (3)
in the case of the matter referred to in (f) above, the same notice as is given to the holders of
such registration rights. Such notice in accordance with the foregoing clause (1) shall also
specify, in the case of any such dividend, distribution or subscription rights, the date on which
the holders of common stock shall be entitled thereto, and such notice in accordance with the
foregoing clause (2) shall also specify the date on which the holders of common stock shall be
entitled to exchange their common stock for securities or other property deliverable upon the
occurrence of such event. Company will also provide information requested by Holder reasonably
necessary to enable Holder to comply with Holder’s accounting or reporting requirements.

          3.3 Registration. The Company agrees that the Shares shall have certain “piggyback”
and “S-3” registration rights pursuant to and as set forth in the Company’s Registration Rights
Agreement dated March 16, 2009 (the “Registration Rights Agreement”), as if for such purpose Holder
(and its successors and assigns to the extent permitted hereunder) were an “Investor” (as used
therein) and the Shares were “Investor Securities” (as used therein). The provisions set forth in
the Registration Rights Agreement relating to the above in effect as of the Restated Warrant Date
may not be amended, modified or waived without the prior written consent of Holder unless such
amendment, modification or waiver affects the rights associated with the Shares in the same manner
as such amendment, modification, or waiver affects the rights associated with all other shares of
the same series and class as the Shares granted to Holder. Holder, Company and the shareholders
party to the Registration Rights Agreement have agreed, pursuant to the Registration Rights
Agreement, that Holder will become a party thereto upon Holder’s exercise or conversion of this
Warrant.

          3.4 No Shareholder Rights. Except as provided in this Warrant, Holder will not have
any rights as a shareholder of the Company until the exercise of this Warrant.

ARTICLE 4. REPRESENTATIONS, WARRANTIES OF HOLDER. Holder represents and warrants to the
Company as follows:

          4.1 Purchase for Own Account. This Warrant and the securities to be acquired upon
exercise of this Warrant by Holder will be acquired for investment for Holder’s account, not as a
nominee or agent, and not with a view to the public resale or distribution within the meaning of
the Act. Holder also represents that Holder has not been formed for the specific purpose of
acquiring this Warrant or the Shares.

          4.2 Disclosure of Information. Holder has received or has had full access to all the
information it considers necessary or appropriate to make an informed investment decision with
respect to the acquisition of this Warrant and its underlying securities. Holder further has had
an opportunity to ask questions and receive answers from the Company regarding the terms and
conditions of the offering of this Warrant and its underlying securities and to obtain additional
information (to the extent the Company

6

 

possessed such information or could acquire it without unreasonable effort or expense) necessary to
verify any information furnished to Holder or to which Holder has access.

          4.3 Investment Experience. Holder understands that the purchase of this Warrant and
its underlying securities involves substantial risk. Holder has experience as an investor in
securities of companies in the development stage and acknowledges that Holder can bear the economic
risk of such Holder’s investment in this Warrant and its underlying securities and has such
knowledge and experience in financial or business matters that Holder is capable of evaluating the
merits and risks of its investment in this Warrant and its underlying securities and/or has a
preexisting personal or business relationship with the Company and certain of its officers,
directors or controlling persons of a nature and duration that enables Holder to be aware of the
character, business acumen and financial circumstances of such persons.

          4.4 Accredited Investor Status. Holder is an “accredited investor” within the meaning
of Regulation D promulgated under the Act.

          4.5 The Act. Holder understands that this Warrant and the Shares issuable upon
exercise or conversion hereof have not been registered under the Act in reliance upon a specific
exemption therefrom, which exemption depends upon, among other things, the bona fide nature of
Holder’s investment intent as expressed herein. Holder understands that this Warrant and the
Shares issued upon any exercise or conversion hereof must be held indefinitely unless subsequently
registered under the Act and qualified under applicable state securities laws, or unless exemption
from such registration and qualification are otherwise available.

ARTICLE 5. MISCELLANEOUS.

          5.1 Term. This Warrant is exercisable in whole or in part at any time and from time
to time on or before the Expiration Date. 

          5.2 Legends. This Warrant and the Shares (and the securities issuable, directly or
indirectly, upon conversion of the Shares, if any) shall be imprinted with a legend in
substantially the following form:

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY
STATE AND, EXCEPT AND PURSUANT TO THE PROVISIONS OF ARTICLE 5 [BELOW][OF THE
WARRANT PURSUANT TO WHICH THESE SHARES WERE ISSUED], MAY NOT BE OFFERED, SOLD OR
OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER
SAID ACT AND APPLICABLE STATE SECURITIES LAW OR, IN THE OPINION OF LEGAL COUNSEL
IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER,
SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION.

          5.3 Compliance with Securities Laws on Transfer. This Warrant and the Shares issuable
upon exercise of this Warrant (and the securities issuable, directly or indirectly, upon conversion
of the Shares, if any) may not be transferred or assigned

7

 

in whole or in part without compliance with applicable federal and state securities laws by the
transferor and the transferee (including, without limitation, the delivery of investment
representation letters and legal opinions reasonably satisfactory to the Company, as reasonably
requested by the Company). The Company shall not require SVB Financial Group to provide an opinion
of counsel if the transfer is to Silicon Valley Bank or any other affiliate of SVB Financial Group.
Additionally, and without limitation on the preceding sentence, if Holder proposes to make such a
transfer or assignment in accordance with Rule 144 under the Act, in lieu of Holder providing an
opinion of counsel in connection with any such proposed transfer or assignment, Holder may provide
representations and warranties in customary form and reasonably satisfactory to the Company
relating to its compliance with Rule 144, and the Company shall cause its legal counsel to issue an
opinion as to the availability of an exemption under Rule 144 with respect to such proposed
transfer or assignment.

          5.4 Transfer Procedure. Subject to the provisions of Article 5.3 and upon providing
the Company with written notice, SVB Financial Group and any subsequent Holder may transfer all or
part of this Warrant or the Shares issuable upon exercise of this Warrant (or the Shares issuable
directly or indirectly, upon conversion of the Shares, if any) to any transferee, provided,
however, in connection with any such transfer, (a) SVB Financial Group or any subsequent Holder
will give the Company notice of the portion of the Warrant being transferred with the name, address
and taxpayer identification number of the transferee, (b) Holder will surrender this Warrant to the
Company for reissuance to the transferee(s) (and Holder if applicable), and (c) the transferee
shall agree to be bound by the restrictions on transfer contained herein and all other provisions
of this Warrant to the same extent as Holder. The Company may refuse to transfer this Warrant or
the Shares to any person who directly competes with the Company, unless, in either case, the stock
of the Company is publicly traded.

          5.5 Notices. All notices and other communications from the Company to Holder, or vice
versa, shall be deemed delivered and effective when given personally or mailed by first-class
registered or certified mail, postage prepaid, at such address as may have been furnished to the
Company or Holder, as the case may (or on the first business day after transmission by facsimile)
be, in writing by the Company or such Holder from time to time. Effective upon receipt of the
fully executed Warrant and the initial transfer described in Article 5.4 above, all notices to
Holder shall be addressed as follows until the Company receives notice of a change of address in
connection with a transfer or otherwise:

SVB Financial Group

Attn: Treasury Department

3003 Tasman Drive, HA 200

Santa Clara, CA 95054

Telephone: 408-654-7400

Facsimile: 408-496-2405

     Notice to the Company shall be addressed as follows until Holder receives notice of a change in
address:

Cardiovascular Systems, Inc.

Attn: Chief Financial Officer

651 Campus Drive

8

 

St. Paul, Minnesota 55112-3495

Telephone: (651) 259-1600

Facsimile: (651) 259-1696

          5.6 Waiver. This Warrant and any term hereof may be changed, waived, discharged or
terminated only by an instrument in writing signed by the party against which enforcement of such
change, waiver, discharge or termination is sought.

          5.7 Attorneys’ Fees. In the event of any dispute between the parties concerning the
terms and provisions of this Warrant, the party prevailing in such dispute shall be entitled to
collect from the other party all costs incurred in such dispute, including reasonable attorneys’
fees.

          5.8 Automatic Conversion upon Expiration. In the event that, upon the Expiration
Date, the fair market value of one Share (or other security issuable upon the exercise hereof) as
determined in accordance with Section 1.3 above is greater than the Warrant Price in effect on such
date, then this Warrant shall automatically be deemed on and as of such date to be converted
pursuant to Section 1.2 above as to all Shares (or such other securities) for which it shall not
previously have been exercised or converted, and the Company shall promptly deliver a certificate
representing the Shares (or such other securities) issued upon such conversion to Holder.

          5.9 Counterparts. This Warrant may be executed in counterparts, all of which together
shall constitute one and the same agreement.

          5.10 Governing Law. This Warrant shall be governed by and construed in accordance
with the laws of the State of Minnesota, without giving effect to its principles regarding
conflicts of law.

[Signature page follows.]

9

 

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	“COMPANY”	 	 	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	CARDIOVASCULAR SYSTEMS, INC.	 	 	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	By:	 	/s/ David Martin	 	 	 	By:	 	/s/ Laurence Betterley	 	 
	 	 	 	 	 	 	 	 	 	 	 
	 

	 	Name:
	 	David Martin
	 	 	 	 	 	Name:
	 	Laurence Betterley	 	 
	 

	 	 	 	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	(Print)
	 	 	 	 	 	 	 	(Print)	 	 
	 

	 	Title:
	 	Chairman of the Board, President or
	 	 	 	 	 	Title:
	 	Chief Financial Officer, Secretary,	 	 
	 

	 	 	 	Vice President
	 	 	 	 	 	 	 	Assistant Treasurer or Assistant	 	 
	 

	 	 	 	 	 	 	 	 	 	 	 	Secretary	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	“HOLDER”	 	 	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	SVB FINANCIAL GROUP	 	 	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	By:	 	/s/ Norman Cutler	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 	 	 	 	 
	 

	 	Name:
	 	Norman Cutler	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	(Print)	 	 	 	 	 	 	 	 	 	 
	 

	 	Title:
	 	Capital Markets Manager	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	 	 	 	 	 	 	 

10

 

SCHEDULE 1

CAPITALIZATION TABLE

Cardiovascular Systems, Inc.

Post-Merger Capitalization

February 25, 2009

	 	 	 	 	 
	 	 	Outstanding
	 
	 	 	 	 
	Common Stock
	 	 	13,744,890	 
	Stock Options
	 	 	3,926,936	 
	Warrants
	 	 	3,134,036	 
	 
	 	 	 	 
	 
	Common Stock outstanding, fully-diluted
	 	 	20,805,862	 
	 
	 	 	 	 

11

 

APPENDIX 1

NOTICE OF EXERCISE

     1. Holder elects to purchase                      shares of the Common/Series                     
Preferred [strike one]
Stock of                                          pursuant to the terms of the attached Warrant, and tenders payment
of the purchase price of the shares in full.

          [or]

     1. Holder elects to convert the attached Warrant into Shares/cash [strike one] in the manner
specified in the Warrant. This conversion is exercised for                                          of the Shares
covered by the Warrant.

     [Strike paragraph that does not apply.]

     2. Please issue a certificate or certificates representing the shares in the name specified
below:

	 	 	 	 	 
	 	 	 
	 	
 	 
	 	Holders Name 	 
	 	      
  	      
      	 	 
	 	
 	 
	 	 	 
	 	
 	 
	 	(Address) 	 
	 	 	 
	 

     3. By its execution below and for the benefit of the Company, Holder hereby restates each of
the representations and warranties in Article 4 of the Warrant as the date hereof.

	 	 	 	 	 
	 	HOLDER:

 	 
	 	
 	 
	 
	 	By:  	
 	 
	 	 	Name:  	 	 
	 	 	Title: 	 	 
	 	 	(Date): 	 	 
	 

12

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