SC 13D/A

UNITED STATES

SECURITIES AND EXCHANGE

 COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 2)*

Cardiovascular Systems, Inc.

 (Name of Issuer)

Common Stock, $0.001 par value per share

(Title of Class of Securities)

141619106

(CUSIP Number)

Michael R. Murphy

Discovery Group I, LLC

191 North Wacker Drive

Suite 1685

Chicago, Illinois 60606

Telephone Number: (312) 265-9600

(Name, Address and Telephone Number of Person

Authorized to Receive Notices and Communications)

September 6, 2011

(Date of Event which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box. o

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See §240.13d-7 for other parties to whom copies are to be sent.

*The remainder of this cover page shall be filled out for a reporting person's initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange Act of 1934 ("Act") or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

CUSIP No. 141619106
	1.	Names of Reporting Persons. Discovery Equity Partners, L.P.
	2.	Check the Appropriate Box if a Member of a Group (See Instructions)
		(a)			o
		(b)			o
	3.	SEC Use Only
	4.	Source of Funds (See Instructions) WC
	5.	Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e)     o
	6.	Citizenship or Place of Organization Illinois
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power None.
			8.	Shared Voting Power 1,157,873
			9.	Sole Dispositive Power None.
			10.	Shared Dispositive Power 1,157,873
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 1,157,873
	12.	Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions)   o
	13.	Percent of Class Represented by Amount in Row (11) 7.1%
	14.	Type of Reporting Person (See Instructions) PN

CUSIP No.  141619106
	1.	Names of Reporting Persons. Discovery Group I, LLC
	2.	Check the Appropriate Box if a Member of a Group (See Instructions)
		(a)			o
		(b)			o
	3.	SEC Use Only
	4.	Source of Funds (See Instructions) AF
	5.	Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e)     o
	6.	Citizenship or Place of Organization Delaware
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power None.
			8.	Shared Voting Power 1,323,315
			9.	Sole Dispositive Power None.
			10.	Shared Dispositive Power 1,323,315
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 1,323,315
	12.	Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions)   o
	13.	Percent of Class Represented by Amount in Row (11) 8.1%
	14.	Type of Reporting Person (See Instructions) IA

CUSIP No.  141619106
	1.	Names of Reporting Persons. Daniel J. Donoghue
	2.	Check the Appropriate Box if a Member of a Group (See Instructions)
		(a)			o
		(b)			o
	3.	SEC Use Only
	4.	Source of Funds (See Instructions) AF
	5.	Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e)     o
	6.	Citizenship or Place of Organization United States of America
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power None.
			8.	Shared Voting Power 1,323,315
			9.	Sole Dispositive Power None.
			10.	Shared Dispositive Power 1,323,315
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 1,323,315
	12.	Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions)   o
	13.	Percent of Class Represented by Amount in Row (11) 8.1%
	14.	Type of Reporting Person (See Instructions) IN

CUSIP No.  141619106
	1.	Names of Reporting Persons. Michael R. Murphy
	2.	Check the Appropriate Box if a Member of a Group (See Instructions)
		(a)			o
		(b)			o
	3.	SEC Use Only
	4.	Source of Funds (See Instructions) AF
	5.	Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e)     o
	6.	Citizenship or Place of Organization United States of America
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power None.
			8.	Shared Voting Power 1,323,315
			9.	Sole Dispositive Power None.
			10.	Shared Dispositive Power 1,323,315
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 1,323,315
	12.	Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions)   o
	13.	Percent of Class Represented by Amount in Row (11) 8.1%
	14.	Type of Reporting Person (See Instructions) IN

Item 1.	Security and Issuer
	This Amendment No. 2 to Schedule 13D (“Amendment No. 2”) relates to the Common Stock, $0.001 par value per share (the “Common Stock”), of Cardiovascular Systems, Inc., a Delaware corporation (the “Company”), which has its principal executive offices at 651 Campus Drive St. Paul, Minnesota 55112.  This Amendment No. 2 amends and supplements, as set forth below, the information contained in items 1, 3, 5 and 6 of the Schedule 13D filed by the Reporting Persons with respect to the Company on August 17, 2011, as amended by Amendment No. 1 thereto filed by the Reporting Persons with respect to the Company on August 29, 2011 (as so amended, the “Schedule 13D”).  All capitalized terms used herein but not defined herein have the meanings set forth in the Schedule 13D.  Except as amended by this Amendment No. 2, all information contained in the Schedule 13D is, after reasonable inquiry and to the best of the Reporting Persons’ knowledge and belief, true, complete and correct as of the date of this Amendment No. 2.
Item 3.	Source and Amount of Funds or Other Consideration
	Item 3 of the Schedule 13D is hereby amended to read in its entirety as follows: The total purchase price for the 1,323,315 shares of Common Stock beneficially owned by Discovery Group and Messrs. Donoghue and Murphy as of September 7, 2011 was approximately $17,820,598, and the total purchase price for the 1,157,873 shares of Common Stock beneficially owned by Discovery Equity Partners was approximately $15,570,523.  The source of such funds was the assets of Discovery Equity Partners and another private investment partnership (collectively, the “Partnerships”) over which Discovery Group exercises discretionary investment management authority, including proceeds of margin loans under margin loan facilities maintained in the ordinary course of business by the Partnerships with a broker on customary terms and conditions.  The Partnerships are the legal owner of all of the Common Stock beneficially owned by Discovery Group and Messrs. Donoghue and Murphy.
Item 5.	Interest in Securities of the Issuer
	Item 5 of the Schedule 13D is hereby amended to read in its entirety as follows: The information concerning percentages of ownership set forth below is based on 16,350,698 shares of Common Stock reported outstanding as of May 31, 2011 in the Company’s Registration Statement of Form S-3, filed on June 3, 2011. Discovery Equity Partners beneficially owns 1,157,873 shares of Common Stock as of September 7, 2011, which represents 7.1% of the outstanding Common Stock. Discovery Group beneficially owns 1,323,315 shares of Common Stock as of September 7, 2011, which represents 8.1% of the outstanding Common Stock. Mr. Donoghue beneficially owns 1,323,315 shares of Common Stock as of September 7, 2011, which represents 8.1% of the outstanding Common Stock. Mr. Murphy beneficially owns 1,323,315 shares of Common Stock as of September 7, 2011, which represents 8.1% of the outstanding Common Stock. Discovery Group is the sole general partner of Discovery Equity Partners and has sole discretionary investment authority with respect to the other Partnership’s investment in the Common Stock.  Messrs. Donoghue and Murphy are the sole managing members of Discovery Group.  As a consequence, Discovery Group and Messrs. Donoghue and Murphy may be deemed to share beneficial ownership of all of the shares of Common Stock owned by both of the Partnerships, while Discovery Equity Partners shares beneficial ownership with Discovery Group and Messrs. Donoghue and Murphy of only the shares of Common Stock owned by it.
	The transactions in Common Stock effected by the Reporting Persons since the date of the most recent filing on Schedule 13D are set out in Exhibit 1 hereto. No person other than the Partnerships is known to any Reporting Person to have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, any of the shares of Common Stock reported herein.
Item 6.	Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer
	Item 6 of the Schedule 13D is hereby amended to read in its entirety as follows: There are no contracts, arrangements, understandings or relationships (legal or otherwise) between or among any of the Reporting Persons and any other person with respect to any securities of the Company other than the governing documents of Discovery Group and the Partnerships, the margin loan facilities referred to under Item 3 of the Schedule 13D, the Joint Filing Agreements of the Reporting Persons with respect to the Schedule 13D that were included as exhibits thereto, the Joint Filing Agreement of the Reporting Persons with respect to this Amendment No. 2 included as Exhibit 2 to this Amendment No. 2, and the Powers of Attorney granted by Messrs Donoghue and Murphy with respect to reports under Section 13 of the Securities Exchange Act of 1934, as amended, which Powers of Attorney are included as Exhibit 3 and Exhibit 4, respectively, to this Amendment No. 2.

Item 7.	Material to Be Filed as Exhibits
	Exhibit 1:                                List of transactions by Reporting Persons in the Company’s Common Stock since the date of the most recent filing on Schedule 13D.
	Exhibit 2:                                Joint Filing Agreement dated as of September 8, 2011, by and among Discovery Equity Partners; Discovery Group; Daniel J. Donoghue; and Michael R. Murphy.
	Exhibit 3:                                Power of Attorney of Daniel J. Donoghue, dated as of April 28, 2008.
	Exhibit 4:                                Power of Attorney of Michael R. Murphy, dated as of April 28, 2008.

Signature

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

September 8, 2011

Date

DISCOVERY GROUP I, LLC,

for itself and as general partner of

DISCOVERY EQUITY PARTNERS, L.P.

By:  Michael R. Murphy*

Signature

Michael R. Murphy, Managing Member

Name/Title

Daniel J. Donoghue*

Signature

Daniel J. Donoghue

Name/Title

Michael R. Murphy*

Signature

Michael R. Murphy

Name/Title

*By: /s/ Mark Buckley

Mark Buckley

Attorney-in-Fact for Daniel J. Donoghue

Attorney-in-Fact for Michael R. Murphy

Exhibit Index

Exhibit 1	List of transactions by Reporting Persons in the Company’s Common Stock since the date of the most recent filing on Schedule 13D.
Exhibit 2	Joint Filing Agreement dated as of September 8, 2011, by and among Discovery Equity Partners; Discovery Group; Daniel J. Donoghue; and Michael R. Murphy.
Exhibit 3	Power of Attorney of Daniel J. Donoghue, dated as of April 28, 2008.
Exhibit 4	Power of Attorney of Michael R. Murphy, dated as of April 28, 2008.

EX-1

EXHIBIT 1

TRANSACTIONS SINCE THE DATE OF THE MOST RECENT FILING ON SCHEDULE 13D

The Reporting Persons engaged in the following transactions in shares of Common Stock of the Company since the date of the most recent filing on Schedule 13D.  Such transactions involved the purchase of shares on the NASDAQ Global Market.  The prices reported below reflect the weighted average purchase price of the shares of Common Stock purchased on the relevant date.  The Reporting Persons hereby undertake to provide upon request to the SEC staff full information regarding the number of shares and prices at which each transaction was effected.

Date	Type		Price	Shares
8/29/20111	Purchase	$	14.1414	18960
8/30/20112	Purchase		13.7801	31345
8/31/20113	Purchase		12.8625	48102
8/31/20114	Purchase		13.7402	9500

9/1/20115	Purchase	13.1469	16063
9/2/20116	Purchase	12.8892	17266
9/6/20117	Purchase	12.8220	18628
9/7/20118	Purchase	13.4736	13700

 

1 This transaction was executed in multiple trades at prices ranging from $13.95 - 14.25. 

2 This transaction was executed in multiple trades at prices ranging from $13.52 - 14.02. 

3 This transaction was executed in multiple trades at prices ranging from $12.46 - 13.43. 

4 This transaction was executed in multiple trades at prices ranging from $13.47 - 14.06. 

5 This transaction was executed in multiple trades at prices ranging from $12.98 - 13.35. 

6 This transaction was executed in multiple trades at prices ranging from $12.55 - 13.15. 

7 This transaction was executed in multiple trades at prices ranging from $12.29 - 13.21. 

8 This transaction was executed in multiple trades at prices ranging from $13.24 - 13.60.

EX-2

EXHIBIT 2

JOINT FILING AGREEMENT

The undersigned hereby agree to the joint filing of Amendment No. 2 to the Schedule 13D to which this Agreement is attached.

Dated:  September 8, 2011

DISCOVERY GROUP I, LLC,

for itself and as general partner of

DISCOVERY EQUITY PARTNERS, L.P.

By  Michael R. Murphy*                                             

       Michael R. Murphy

       Managing Member

Daniel J. Donoghue*                                                    

Daniel J. Donoghue

Michael R. Murphy*                                                     

Michael R. Murphy

*By: /s/ Mark Buckley                                                  

         Mark Buckley

         Attorney-in-Fact for Daniel J. Donoghue

         Attorney-in-Fact for Michael R. Murphy

EX-3

EXHIBIT 3

POWER OF ATTORNEY

The undersigned, Daniel J. Donoghue, hereby appoints Mark Buckley his true and lawful attorney-in-fact and agent, with full power to execute and file with the United States Securities and Exchange Commission and any stock exchange or similar authority, for and on his behalf in any and all capacities, any and all reports required to be filed pursuant to Section 13 of the Securities Exchange Act of 1934 and the rules thereunder on Schedule 13D or 13G, any and all amendments to such reports, with all exhibits, and any other forms or documents as may be necessary in connection with the filing of such reports with the United States Securities and Exchange Commission and any stock exchange or similar authority, granting unto said attorney full power and authority to do and perform any and all acts for and on behalf of the undersigned which may be necessary or desirable to complete, as fully as the undersigned might or could do in person.

This Power of Attorney shall remain in full force and effect until revoked by the undersigned in a signed writing delivered to the foregoing attorney-in-fact and agent.

IN WITNESS WHEREOF the undersigned has caused this Power of Attorney to be executed this 28th day of April, 2008.

/s/ Daniel J. Donoghue

Daniel J. Donoghue

STATE OF ILLINOIS	)
	)	SS.
COUNTY OF COOK	)

 

I, Kareema M. Cruz, a Notary Public in and for the County of Cook, State of Illinois, DO HEREBY CERTIFY that Daniel J. Donoghue, who is personally known to me to be the same person whose name is subscribed to the foregoing instrument, appeared before me this day in person and acknowledged that he signed and delivered the said instrument as his own free and voluntary act, for the uses and purposes therein set forth.

Given under my hand and notarial seal, this 28th day of April, 2008.

/s/ Kareema M. Cruz

Notary Public

EX-4

EXHIBIT 4

POWER OF ATTORNEY

The undersigned, Michael R. Murphy, hereby appoints Mark Buckley his true and lawful attorney-in-fact and agent, with full power to execute and file with the United States Securities and Exchange Commission and any stock exchange or similar authority, for and on his behalf in any and all capacities, any and all reports required to be filed pursuant to Section 13 of the Securities Exchange Act of 1934 and the rules thereunder on Schedule 13D or 13G, any and all amendments to such reports, with all exhibits, and any other forms or documents as may be necessary in connection with the filing of such reports with the United States Securities and Exchange Commission and any stock exchange or similar authority, granting unto said attorney full power and authority to do and perform any and all acts for and on behalf of the undersigned which may be necessary or desirable to complete, as fully as the undersigned might or could do in person.

This Power of Attorney shall remain in full force and effect until revoked by the undersigned in a signed writing delivered to the foregoing attorney-in-fact and agent.

IN WITNESS WHEREOF the undersigned has caused this Power of Attorney to be executed this 28th day of April, 2008.

/s/ Michael R. Murphy  

Michael R. Murphy

STATE OF ILLINOIS	)
	)	SS.
COUNTY OF COOK	)

I, Kareema M. Cruz, a Notary Public in and for the County of Cook, State of Illinois, DO HEREBY CERTIFY that Michael R. Murphy, who is personally known to me to be the same person whose name is subscribed to the foregoing instrument, appeared before me this day in person and acknowledged that he signed and delivered the said instrument as his own free and voluntary act, for the uses and purposes therein set forth.

Given under my hand and notarial seal, this 28th day of April, 2008.

/s/ Kareema M. Cruz

Notary Public