Cardiovascular Systems, Inc.Redefining Interventional Vascular Solutions

Annual Meeting of Stockholders

November 16, 2016

Safe Harbor

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FORWARD-LOOKING STATEMENTSCertain statements made in this presentation are forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995 and are provided under the protection of the safe harbor for forward-looking statements provided by that Act. In some cases, you can identify forward-looking statements by terms such as “may,” “will,” “should,” “could,” “would,” “expect,” “plans,” “anticipates,” “believes,” “estimates,” “projects,” “predicts,” “potential” and similar expressions intended to identify forward-looking statements. Examples of these statements include, but are not limited to, statements regarding Cardiovascular System, Inc.’s (“CSI” or the “Company”) future financial performance, product sales distribution, industry and market expectations and estimates, the benefits and uses of the Company’s products, market opportunity potential, clinical trials, international expansion, regulatory approvals, future profitability, debt capacity, use of proceeds, results of operations, prospects, plans and

objectives of management, and other statements that are other than statements of historical fact.

These statements involve risks and uncertainties which could cause results to differ materially from those projected, including those described under the heading “Risk Factors” contained in the prospectus filed with the Securities and Exchange Commission (the “SEC”) for our recent public offering, and as detailed from time to time in CSI’s SEC reports, including its Reports on Form 10-K and Form 10-Q. As a result of these matters, changes in facts, assumptions not being realized or other circumstances, CSI's actual results may differ materially from the expected results discussed in the forward-looking statements presented. The forward-looking statements are made only as of the date of this presentation, and CSI undertakes no obligation to update them to reflect subsequent events or circumstances.

Fiscal Year 2016 Achievements

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• Refined sales strategy and stabilized sales force• Resumed sequential quarterly sales growth• Successfully transitioned the senior leadership team• Settled the DOJ investigation• Lowered operating expenses• Significantly reduced quarterly net loss• Positioned CSI for revenue growth, positive cash flow and

profitability

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$0

$50

$100

$150

$200

FY12 FY13 FY14 FY15 FY16 Q1 FY17

Revenue Growth From CSI Products *FY16 Slowed by Sales Force Transition

Return to Growth in FY17

$ in

Mill

ion

s

* CSI Products exclude revenue from distribution agreement terminated on June 30, 2015

14% Growth

21% CAGR

Strong, Improving Gross Margins

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70%

75%

80%

85%

FY12 FY13 FY14 FY15 FY16 Q1 FY17

78.2%

80.1%

76.5%77.3%

76.7%

81.0%

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$20

$30

$40

$50

$60

Q1 FY16 Q2 FY16 Q3 FY16 Q4 FY16 Q1 FY 17

Declining Operating ExpensesCost Realignment, Reduction in Workforce

$ in

Mill

ion

s

Q3 FY16 operating expenses include $12.4 million of one-time costs for DOJ settlement/severance

-13% From Prior Year

One-Time Costs

Achieved Positive Adjusted EBITDA

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$41.4$44.5

$48.5 $49.8

Q2 '16 Q3 '16 Q4 '16 Q1 '17

-$11.1

-$6.4

-$1.4

$2.6

Q2 '16 Q3 '16 * Q4 '16 Q1 '17

Revenue Adjusted EBITDA

* Excludes $12.2 million of DOJ settlement and severance costs (net of stock-based compensation)

$ in millions

Reconciliations of Adjusted EBITDA to the most comparable U.S. GAAP measure for the respective periods can be found in the appendix

Solid Cash Position/No Debt

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$84

$65$61 $58

$68

$0

$20

$40

$60

$80

$100

Q4 FY15 Q2 FY16 Q4 FY16 Q1 FY17 Q1 FY17Pro-forma*

Cash Adequate to Reach Positive Cash Flow and Profitability

$ M

illio

ns

• Decreasing cash burn from cost reductions/increasing revenues• Positive cash flow in Q1 FY17 excluding $3M DOJ payment• $10M upfront payment received for Japan Distribution Rights (Nov. 2016)• Additional cushion potential from facility financing/debt capacity

*Includes $10M upfront payment for Japan distribution rights

Sales Force Stabilization

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240 Professionals

Rev

en

ue

Pe

r Sa

les

Pro

fess

ion

al

• One sales force selling two, high-margin, high-growth products• Deeper adoption into fewer high potential accounts• Higher productivity per sales professional• Drives future profitability

Leadership in Clinical Evidence

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LIBERTY 360°(Enrollment Complete)

ORBIT II(3-year Data)

COAST(Enrollment Complete)

OASIS, CONFIRM series, CALCIUM 360 and COMPLIANCE 360

• Supports 2nd Gen OAS in U.S. and Japan approval• Shonin application submitted in June 2016

• 92% freedom from revascularization at 3-years• Up to $4,946 per patient cost savings at 2-years

• High rates of procedural success and durability• Low adverse events/bail-out stenting

• “All-comers” trial vs. any other treatment• Nearly 700 Rutherford class 4, 5, or 6

n=1,204

n=100

Trial ImportanceSize

n=3,359

PAD

CA

D

n=443

Patients Lesions Physicians

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OPTIMIZE (Enrolling)

n=50 • OAS + DCB vs. DCB alone• Calcified below-the-knee lesions

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ECLIPSE(Enrollment Begins 2017)

• Largest randomized trial to study coronary atherectomy for calcified coronary lesions

• OAS + DES vs. angioplasty + DESn=2,000

LIBERTY 360° Acute/30-Day Results

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• Diamondback OAS was the most frequently used atherectomy device across all Rutherford Classes

• Physicians reported high satisfaction regarding device selection and patient outcome

• 78% of Rutherford 6 patients were discharged to their homes• Favorable freedom from Major Adverse Events (MAE) and

Target Vessel Revascularization (TVR)

Rutherford Class

Freedom from MAE at 30 Days

Freedom from TVR at 30 Days

2-3 99.0% 99.4%

4-5 95.7% 96.9%

6 90.7% 97.9%

Principal investigators: Philippe Généreux, Ajay Kirtane; Study chairman: Gregg W. StoneSponsor: Cardiovascular Systems Inc.

Orbital Atherectomy Strategy

(1.25 mm Crown followed by non-compliant balloon optimization)

Conventional Angioplasty Strategy

(conventional and/or specialty balloons per operator discretion)

2nd generation DES implantation and optimization

2nd generation DES implantation and optimization

Randomize1:1

Primary endpoints: 1) Post-PCI minimal stent area assessed by OCT (N≈400 in imaging study) 2) 1-year TVF (all patients)

≈2000 pts with severely calcified lesions; ≈60 US sites

ECLIPSE Trial DesignEvaluation of Treatment Strategies for Severe CaLcifIc Coronary Arteries:

Orbital Atherectomy vs. Conventional Angioplasty Prior to Implantation of Drug Eluting StEnts

Consistent, Attractive Reimbursement

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Hospital Procedure 2017 Reimbursement% Change from 2016

Inpatient PAD $10,593-$19,754 4%-3%

Inpatient CAD $10,072-$19,396 1%-1%

Outpatient PAD/CAD $9,727-$14,511 2%-(1%)

Non-Hospital Facility

Procedure * 2017 Reimbursement% Changefrom 2016

Outpatient PAD (ATK) $10,957-$14,853 (2%)-(2%)

Outpatient PAD (BTK) $10,804-$13,371 (2%)-(2%)

* Procedures using atherectomy

MS-DRG 246, 247, 248, 249, 250, 251, 252, 253, 254; CPT Codes 37225, 37227, 37229, 37231, 92933; C-APCs 5191,5192,5193,5194; HCPCS Code C9602

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• CSI is the market leader in peripheral and coronary atherectomy • OAS treats untreatable patients with calcified lesions • CSI supports physicians with an expanding portfolio of

compelling medical evidence• Reimbursement for our atherectomy procedures remains stable • We can maintain strong, steady gross margins• CSI’s sales force, now stabilized, is a significant asset • Improving productivity combined with expense control

demonstrates a strong business model poised for future profitability.

Renewed Confidence

DIAMONDBACK 360® Coronary Orbital Atherectomy System

Indications: The DIAMONDBACK 360® Coronary Orbital Atherectomy System (OAS) is a percutaneous orbital atherectomy system indicated to facilitate stent delivery in patients with coronary artery disease (CAD) who are acceptable candidates for PTCA or stenting due to de novo, severely calcified coronary artery lesions.

Contraindications: The OAS is contraindicated when the VIPERWIRE guide wire cannot pass across the coronary lesion or the target lesion is within a bypass graft or stent. The OAS is contraindicated when the patient is not an appropriate candidate for bypass surgery, angioplasty, or atherectomy therapy, or has angiographic evidence of thrombus, or has only one open vessel, or has angiographic evidence of significant dissection at the treatment site and for women who are pregnant or children.

Warnings/Precautions:; Performing treatment in excessively tortuous vessels or bifurcations may result in vessel damage; The OAS was only evaluated in severely calcified lesions, A temporary pacing lead may be necessary when treating lesions in the right coronary and circumflex arteries; On-site surgical back-up should be included as a clinical consideration; Use in patients with an ejection fraction (EF) of less than 25% has not been evaluated. See the instructions for use before performing DIAMONDBACK 360 coronary orbital atherectomy procedures for detailed information regarding the procedure, indications, contraindications, warnings, precautions, and potential adverse events. For further information call CSI at 1-877-274-0901 and/or consult CSI’s website at www.csi360.com.

Caution: Federal law (USA) restricts this device to sale by or on the order of a physician.

Diamondback 360® and Stealth 360®Peripheral Atherectomy Systems

The Diamondback 360® and Stealth 360® PAD Systems are percutaneous orbital atherectomy systems indicated for use as therapy in patients with occlusive atherosclerotic disease in peripheral arteries and stenotic material from artificial arteriovenous dialysis fistulae. The Systems arecontraindicated for use in coronary arteries, bypass grafts, stents, or where thrombus or dissections are present. Although the incidence of adverse events is rare, potential events that can occur with atherectomy include: pain, hypotension, CVA/TIA, death, dissection, perforation, distal embolization, thrombus formation, hematuria, abrupt or acute vessel closure, or arterial spasm. For further information call CSI at 1-877-274-0901 and/or consult CSI’s website at www.csi360.com.

Caution: Federal law (USA) restricts this device to sale by or on the order of a physician.

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Appendix

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Adjusted EBITDA Reconciliation

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Non-GAAP Financial MeasuresTo supplement CSI's presentation prepared in accordance with GAAP, CSI uses a non-GAAP financial measure referred to as "Adjusted EBITDA" in this presentation. Reconciliations of Adjusted EBITDA to the most comparable U.S. GAAP measure for the respective periods can be found here. In addition, an explanation of the manner in which CSI's management uses Adjusted EBITDA to conduct and evaluate its business, the economic substance behind management's decision to use Adjusted EBITDA, the substantive reasons why management believes that Adjusted EBITDA provides useful information to investors, the material limitations associated with the use of Adjusted EBITDA and the manner in which management compensates for those limitations can be found in CSI’s most recent quarterly earnings release, dated, Oct. 26, 2016.

Three Months EndedDec. 31,

2015Mar. 31, 2016 June 30, 2016 Sept. 30, 2016

Net Loss $(15,163) $(22,716) $(4,884) $ (1,856)

Less: Other (Income) Expense, net (3) (33) (111) (33)

Less: Provision for income taxes 23 23 23 24

Loss from Operations (15,143) (22,726) (4,972) (1,867)

Add: Stock-based compensation 3,112 3,173 2,585 3,450

Add: Depreciation and amortization 981 979 1,017 1,017

Adjusted EBITDA (11,050) (18,574) (1,370) 2,600

Add: One-time costs (net of stock-based compensation) * - 12,218 - -

Adjusted EBITDA (net of one-time costs) $(11,050) $(6,356) $(1,370) $2,600

* One-time costs include: Department of Justice settlement, restructuring charges from a workforce reduction, and CEO retirement benefits.

Pro-Forma Cash Reconciliation

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$ in millions

Cash and cash equivalents as of Sept. 30, 2016 $58

Add: Upfront payment received from Medikit for exclusive distribution rights in Japan (November 2016)

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Q1 FY17 Pro-forma cash position * $68

Investor Contact:Jack NielsenSenior Director Corporate Communications & Investor Relations651-202-4919j.nielsen@csi360.com

©2016 Cardiovascular Systems, Inc.All Rights ReservedDiamondback 360 and CSI are registered trademarks of Cardiovascular Systems, Inc.www.csi360.com

NASDAQ: CSII

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