MODIFICATION NO. 3 TO LOAN AND SECURITY AGREEMENT

EXHIBIT 10.54

MODIFICATION NO. 3 TO LOAN AND SECURITY AGREEMENT

This Modification No. 3 to Loan and Security Agreement (“Modification”) is entered into as of June 30, 2012 (the “Modification No. 3 Effective Date”), by and between Partners for Growth III, L.P., a Delaware limited partnership with its principal place of business at 150 Pacific Avenue, San Francisco, California 94111 (“PFG”) and Cardiovascular Systems, Inc., Inc., a Delaware corporation with its principal place of business at 651 Campus Drive, St. Paul, MN 55112 (“Borrower”).

WHEREAS, PFG and Borrower entered into that certain Loan and Security Agreement dated as of April 14, 2010 (the “Loan Agreement”) and certain other Security Documents (as defined below), pursuant to which Borrower has borrowed and PFG has loaned pursuant to Convertible Promissory Notes up to $4,000,000 at any one time outstanding;

WHEREAS, the parties entered into that certain Modification No. 1 to Loan and Security Agreement dated as of August 23, 2011 (the “First Modification”);

WHEREAS, the parties entered into that certain Modification No. 2 to Loan and Security Agreement dated as of December 27, 2011 (the “Second Modification” and, together with the First Modification, the “Prior Modifications”);

WHEREAS, Borrower and the Senior Lender are amending the Senior Loan Documents and such amendment requires a facilitating amendment of the Loan Agreement;

NOW THEREFORE, the parties hereby agree as follows:

1. DESCRIPTION OF EXISTING INDEBTEDNESS: Borrower is indebted to PFG for Obligations pursuant to the Loan Documents. The Loan Agreement provides for the issuance of up to $5,000,000 in Notes to PFG from time to time, of which an aggregate principal amount of $5,000,000 in Notes are issued and outstanding on the date of this Modification. Defined terms used but not otherwise defined herein shall have the same meanings set forth in the Loan Agreement.

2. DESCRIPTION OF COLLATERAL. Repayment of the Obligations is secured by the Collateral, as described in the Loan Agreement and an Intellectual Property Security Agreement of even date therewith. The above-described security documents, together with all other documents securing repayment of the Obligations, shall be referred to herein as the “Security Documents”. Hereinafter, the Security Documents, together with all other documents evidencing or securing the Obligations are referred to as the “Existing Loan Documents”.

3. MODIFICATION TO LOAN AGREEMENT. The Schedule is hereby amended as follows:

3.1 Section 1(d). Section 1(d) which prior to the Modification No. 3 Effective Date read as follows (italicized for ease of reference):

shall be replaced in its entirety with and read prospectively with effect from the Modification No. 3 Effective Date, as follows:

3.2 Liquidity Ratio. The Liquidity Ratio covenant set forth in Section 5(a) of the Schedule which prior to the Modification No. 3 Effective Date read as follows (italicized for ease of reference):

shall be replaced in its entirety with and read prospectively with effect from the Modification No. 3 Effective Date, as follows:

3.3 EBITDA; Fixed Charge Coverage Ratio. The EBITDA and Fixed Charge Coverage Ratio covenants set forth in Section 5(b) of the Schedule which prior to the Modification No. 3 Effective Date read as follows (italicized for ease of reference):

shall be replaced in its entirety with and read prospectively with effect from June 30, 2012, as follows:

4. CONSISTENT CHANGES. The Existing Loan Documents are hereby amended wherever necessary to reflect the changes described above.

5. PAYMENT OF LOAN FEE AND EXPENSES. Borrower shall pay to PFG all of PFG’s reasonable and documented out-of-pocket costs and expenses in connection with this Modification.

6. BORROWERS’ REPRESENTATIONS AND WARRANTIES. Borrower represents and warrants that:

(a) immediately upon giving effect to this Modification (i) except for the matters set forth in Exhibit A and in the capitalization table appended hereto as Exhibit B, the representations and warranties contained in the Loan Agreement are true, accurate and complete in all material respects as of the date hereof (except to the extent such representations and warranties relate to an earlier date, in which case they are true and correct as of such date), and (ii) no Event of Default has occurred and is continuing;

(b) Borrower has the corporate power and authority to execute and deliver this Amendment and to perform its obligations under the Existing Loan Documents, as amended by this Modification;

(c) the certificate of incorporation, bylaws and other organizational documents of Borrower delivered to PFG remain true, accurate and complete and have not been amended, supplemented or restated and are and continue to be in full force and effect;

(d) the execution and delivery by Borrower of this Modification and the performance by Borrower of its obligations under the Existing Loan Documents, as amended by this Modification, have been duly authorized by all necessary corporate action on the part of Borrower;

(e) this Modification has been duly executed and delivered by Borrower and is the binding obligation of Borrower, enforceable against it in accordance with the terms of this Modification, 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;

(f) as of the date hereof, Borrower has no defenses against its obligation to repay the Obligations and it has no claims of any kind against PFG. Borrower acknowledges that PFG has acted in good faith and has conducted in a commercially reasonable manner its relationship with such Borrower in connection with this Modification and in connection with the Existing Loan Documents;

(g) the Security Documents relating to Intellectual Property either disclose an accurate, complete and current listing of all Collateral that consists of Intellectual Property or Borrower has included revised and updated Intellectual Property schedules as part of an update to the Representations required in Section 8 of this Modification; and

(h) as of the date hereof, except for the matters set forth in Exhibits A and B hereto, Borrower ratifies, confirms and reaffirms, all and singular, the terms and disclosures contained in the Representations dated as of August 8, 2011, and as of the date Borrower makes a request to issue a Note on or after the date hereof, Borrower shall ratify, confirm and reaffirm, all and singular, the terms and disclosures contained in the Representations dated as of August 8, 2011 as modified by Exhibits A and B hereto, and shall acknowledge, confirm and agree that the disclosures and information Borrower provided to PFG in Part A—Sections 1-6 (except as further noted in this sentence) and Part B—Sections 11, 12 and 13 of the Representations shall not have changed as of the date of such borrowing request, and all other Sections of the Representations, including Part A Section 3(d),(e) (g) and (i) shall have not changed as of such borrowing request in any material respect or, if the Representations require additional disclosure in order to be true, accurate and complete as of the date hereof, Borrower shall have provided the update to the Representations required in Section 8 hereof.

Borrower understands and acknowledges that PFG is entering into this Modification in reliance upon, and in partial consideration for, the above representations and warranties, and agrees that such reliance is reasonable and appropriate.

7. CONTINUING VALIDITY. Borrower understands and agrees that in modifying the existing Obligations, PFG is relying upon Borrower’s representations, warranties, and agreements, as set forth in the Existing Loan Documents. Except as expressly modified pursuant to this Modification, the terms of the Existing Loan Documents remain unchanged and in full force and effect. PFG’s agreement to modifications to the existing Obligations in no way shall obligate PFG to make any future consents, waivers or modifications to the Obligations. Nothing in this Modification shall constitute a satisfaction of the Obligations or a waiver of any default under the Existing Loan Documents. It is the intention of PFG and Borrower to retain as liable parties all makers and endorsers of Existing Loan Documents, unless the party is expressly released by PFG in writing. Unless expressly released herein, no maker, endorser, or guarantor will be released by virtue of this Modification. The terms of this paragraph apply not only to this Modification, but also to all subsequent loan modification agreements.

8. CONDITIONS. The effectiveness of this Modification is conditioned upon each of:

(a) Execution and Delivery. Borrower shall have duly executed and delivered to PFG a counterpart of this Modification and a true and correct copy of the Senior Loan Documents, as amended to the Modification No. 3 Effective Date.

(b) Payment of PFG Expenses. Borrower shall have paid upon demand all PFG expenses (including all reasonable attorneys’ fees and expenses) incurred in connection with this Modification in accordance with Section 5 hereof.

(c) Updates to Borrower Information. On or prior to the date of any request for borrowing on or after the date hereof, Borrower shall have certified its compliance with Section 6(h), or, if required to render Part A—Sections 1-6 (except Section 3(d),(e) (g) and (i)) and Part B—Section 11 of the Representations identified in Section 7(i) hereof true, correct, accurate and complete as of the date hereof, and all other Sections of the Representations, including Part A Section 3(d),(e) (g) and (i) true, correct, accurate and complete in all material respects as of the date of such borrowing request, shall have delivered to PFG true and current information and versions of such documents.

(d) No Default under Senior Debt Documents. There shall be no default under the Senior Debt Documents that has not been cured or waived.

(e) SVB Subordination. PFG and the Senior Lender shall have entered into an amendment to or ratification of their existing Subordination Agreement reflecting the amendment to the Senor Loan Documents.

9. FURTHER ASSURANCES. Borrower agrees to execute such further documents and instruments and to take such further actions as PFG may request in its good faith business judgment to carry out the purposes and intent of this Modification.

10. INTEGRATION; CONSTRUCTION. The Loan Agreement, the Prior Modifications, this Modification and any documents executed in connection therewith and herewith contain the entire agreement between the parties with respect to the subject matter hereof and supersede all prior agreements, understandings, offers and negotiations, oral or written, with respect thereto and no extrinsic evidence whatsoever may be introduced in any judicial or arbitration proceeding, if any, involving this Modification; provided, however, that any financing statements or other agreements or instruments filed by PFG with respect to Borrower shall remain in full force and effect. The quotation marks around modified clauses set forth herein and any differing font styles in which such clauses are presented herein are for ease of reading only and shall be ignored for purposes of construing and interpreting this Modification. This Modification is subject to the General Provisions of Section 8 of the Loan Agreement.

11. GOVERNING LAW; VENUE. THIS MODIFICATION SHALL BE GOVERNED BY AND SHALL BE CONSTRUED AND ENFORCED IN ACCORDANCE WITH THE LAWS OF THE STATE OF CALIFORNIA. Borrower and PFG submit to the exclusive jurisdiction of the State and Federal courts in San Francisco County, California, in connection with any proceeding or dispute arising in connection herewith.

This Modification is executed as of the date first written above.

[Signature Page Follows]

Signature Page Modification No. 3 to Loan and Security Agreement

EXHIBIT A

EXCEPTIONS TO REPRESENTATIONS AND WARRANTIES

A. Litigation

1. Michael Kallok. On July 18, 2011, the Company received a demand letter from legal counsel for Michael Kallok, a former officer, director and consultant to the Company, claiming that Mr. Kallok is entitled to 42,594 shares of the Company’s common stock or, alternatively, the value of those shares as of July 15, 2011, which was $610,798. Mr. Kallok asserts that the Company improperly deemed such shares forfeited under a restricted stock agreement with Mr. Kallok. The Company disagrees with Mr. Kallok’s claim and the parties are moving forward with arbitration to resolve this matter.

2. Litigation in Switzerland. In July 2009, the Company commenced a lawsuit in Switzerland against Dr. Leonid Shturman (“Dr. Shturman”), primarily to halt the grant proceedings before the European Patent Office. The Company asserted that it was the owner of the counterweight invention included in the European patent application No. 06 745 024.7 filed by Dr. Shturman. On April 15, 2011, Dr. Shturman’s widow, Leila Nadirashvili, filed a writ to dismiss the Company’s lawsuit based on res judicata and collateral estoppel, alleging that the claims in Switzerland are identical to a previously-dismissed lawsuit in Minnesota. The Company successfully defeated the motion. On June 21, 2012 the parties reached a settlement whereby Ms. Nadirashvili assigned the patent application to the Company.

3. Litigation in the United States District Court in Minnesota. On August 24, 2011, Leila Nadirashvili was substituted as plaintiff in a lawsuit in the United States District Court in Minnesota. The lawsuit seeks to enjoin the litigation in Switzerland discussed above. Ms. Nadirashvili declined the Company’s offer of settlement. In December 2011, the Court dismissed the lawsuit on the grounds that the Court lacked jurisdiction.

4. Litigation in the United States District Court in Minnesota. On August 24, 2011, Leila Nadirashvili commenced a lawsuit against the Company in the United States District Court in Minnesota. In the lawsuit, Ms. Nadirashvili is asserting declaration of patent ownership, slander of title, tortious interference with prospective business relations, and unfair competition in violation of Minnesota Statute § 324D.44. In December 2011, the Court dismissed the lawsuit on the grounds that the Court lacked jurisdiction.

5. Litigation in the United States District Court in Minnesota. In February 2012, Ms. Nadirashvili re-filed her lawsuit against the Company in Hennepin County District Court. The Company removed the lawsuit to the United States District Court in Minnesota. In the lawsuit, Ms. Nadirashvili seeks a declaration that she is the sole owner of six United States patents that have issued naming Dr. Leonid Shturman as the sole inventor. In addition, Ms. Nadirashvili has asserted claims for slander of title, tortious interference with prospective business relations, and unfair competition. Ms. Nadirashvili seeks an unspecified sum of damages. The Company asserted counterclaims seeking a declaration that the patents are invalid, imposition of a constructive trust, and unjust enrichment damages. A settlement conference has been scheduled to occur on August 14, 2012.

B. Officers and Directors

1. Scott Kraus has been replaced as Vice President of Sales by Jim Briedenstein.

2. Paul Koehn’s title has been changed from Vice President of Manufacturing to Vice President of Quality and Manufacturing.

3. Dr. Geoffrey Hartzler passed away on March 10, 2012 and so no longer serves as a director.

EXHIBIT B

Capitalization Table 6/20/2012

There are 604,126 remaining shares available for grant under the 2007 Equity Plan.

There are 90,709 available shares for purchase through the Employer Stock purchase plan.

The Company has $5.0MM in outstanding loans under a convertible debt facility with Partners for Growth III, L.P. (PFG). At any time prior to the maturity date, PFG may at its option convert any of the outstanding loans into shares of the Company’s common stock at the applicable conversion price. In aggregate, the outstanding loans can be converted into 363,794 shares of the Company’s common stock.

DETAIL