Cardiovascular Systems, Inc.NASDAQ: CSII

San Francisco Investor MeetingsJanuary 11, 2017

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.

Investment Merits

• Orbital atherectomy addresses calcified arterial plaque - a large, unmet medical need

• Three attractive markets:– Peripheral - below the knee

– Peripheral - above the knee

– Coronary

• Medical evidence and stable reimbursement support growth

• Early stage of adoption; large, clinically trained sales force

• Positioned for sustainable, profitable revenue growth

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4

Benefits of Orbital Atherectomy

Above the Knee

Heart

Below the Knee3

With systems for coronary or peripheral indications, the CSI product line offers heart-to-heels capability.

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3• Heart-to-heels solution• Effective in calcium• Excellent safety• Alternate access sites• Long-term durability• Economical

Crowns shown are not to scale and for illustrative purposes only.

CSI Orbital Atherectomy Systems (OAS)Differential Sanding:

• Eccentrically mounted crown bi-directionally sands hard plaque

• Healthy, elastic tissue flexes away from crown to minimize vessel damage

Centrifugal Force:

• Increasing speed = increased orbit radius

• 360° crown contact designed to create a smooth, concentric lumen

• Allows constant blood flow and particulate flushing during orbit

• Treat large vessels through small sheaths, multiple vessels with one crown

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Peripheral Application: Before & After

Anterior tibial90% occluded

Before After

< 5% residualSmooth, tubular

lumen

Case courtesy of Dr. Jihad Mustapha, Metro Health (Results may vary)

Plaque safely removed, blood

flow restored with durable

results

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• 93% < red blood cell size

• 99% < lumen size of capillaries

Unique Mechanism of ActionBi-directional and differential sanding

Calculation of mean particulate size is based particles larger than 1 micron from a representative study using carbon blocks and cadaver model systems. 7

Only 2.6 Million Receiving Treatment

700,000 CLI

Peripheral Artery Disease (PAD)Large and underserved patient population

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Sources: Sage Group, Millennium Research Group “US Markets for Peripheral Intervention Devices 2014,” iData “US Market for Peripheral Vascular Devices and Accessories” 2014, and Go, et al “Heart Disease and Stroke Statistics -- 2014 Update,” Circulation.

1.9 Million Claudicant

Up to 18 Million in U.S. with PAD, ≈4 Million with Critical Limb Ischemia

(CLI)

2.6 Million Treated

≈750,000 Below The Knee

(BTK) Treatments

≈1.8 MillionAbove The Knee

(ATK)Treatments

BTK Calcium ≈ $1B Opportunity

*CSI estimates

130,000 Amputations

170,000 Interventions

450,000Medical

Management

120,000 Interventions

120,000 Amputations

60,000 Medical

Management

≈750,000 Below The Knee (BTK) Treatments

≈300,000* Patients with Calcified Lesions BTK

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ATK Calcium ≈ $1B Opportunity

30,000 Amputations

300,000 Interventions

1.5M Medical

Management

150,000 Interventions

30,000 Amputations

100,000 Medical

Management

≈280,000* Patients with Calcified Lesions ATK

≈1.8 Million Above the Knee(ATK) Treatments

*CSI estimates

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J Invasive Cardiol. 2000; 12(11)

1 Fitzgerald PJ, et al.. Circulation. 1992:86;64-70. Kahn J, et al. Cathet Cardiovasc Diagn. 1990;21:89-91.2 Cavusoglu E, et al. Cathet Cardivasc Intervent. 2004;62:485-498.3 Moussa I, et al. Circulation. 1997;96(1):128-136. 4 Gilutz H, et al. Cathet Cardiovasc Intervent. 2000;50:212-214.5 Nakano M, et al. Eur Heart J. 2013;34:3304-3313.6 Buckley CJ. Vascular Disease Management. 2011;8:87-92.

Calcified Coronary Lesions

• Prone to dissection during balloon angioplasty or pre-dilatation1

• Difficult to completely dilate2

• May prevent adequate stent expansion3

• Prevent stent delivery to the desired location4

• Uneven drug distribution associated with restenosis5

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CAD Severe Calcium ≈ $700M Opportunity

880,000PCI

250,000 CABG

CABG, 250M

* 12% severe calcium in both PCIs & CABG + 48,000 estimated CHIP patientsBourantas,C et al; Heart, 2014;0:1–7. 20% severe Ca++ in DES trialsGénéreux, P. et al. J Am Coll Cardiol 2014;63(18):1845-54. 6% severe Ca++ in ACSFeldman D. et al, Circulation. 2013;127:2295-2306. 60% of PCIs ACS, 40% stable 12% severe Ca++

100,000 PCI

30,000CABG

≈178,000* Patients with Severely Calcified Lesions

≈1.25 Million Coronary Artery Disease (CAD) Procedures and Estimated CHIP Patients

48,000CHIP Patients

CHIP: Complex Higher-Risk Indicated Patients

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120,000CHIP Patients

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

5000+Patients

7000Lesions

600Physicians

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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

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%

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

• Physicians reported high satisfaction regarding device selection and patient outcome

• Favorable freedom from Major Adverse Events (MAE) and Target Vessel Revascularization (TVR)

• 78% of Rutherford Class 6 patients released to home

LIBERTY 360° Study Design/30-Day ResultsStudy Design

30-Day Results

Adams, LIBERTY Late Breaking Clinical Trial, AMP Conference, Aug 11, 2016. 14

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

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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%)

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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$0

$50

$100

$150

$200

FY12 FY13 FY14 FY15 FY16 Q1 FY17

Track Record of Revenue Growth FY16 Slowed by Sales Force Transition

Return to Growth in FY17

$ M

illio

ns

Amounts exclude revenue from distribution agreement terminated on June 30, 2015

+14%

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%

Solid Cash Position/No DebtCash Adequate to Reach Positive Cash Flow and Profitability

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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*

$ 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

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 litigation and severance costs.

$ millions

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

Why CSI?

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• Orbital atherectomy addresses calcified arterial plaque - a large, unmet medical need

• Three attractive markets:– Peripheral - below the knee

– Peripheral - above the knee

– Coronary

• Medical evidence and stable reimbursement support growth

• Early stage of adoption; large, clinically trained sales force

• Positioned for sustainable, profitable revenue growth

Appendix

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Adjusted EBITDA Reconciliation

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Non-GAAP Financial MeasuresTo supplement CSI's consolidated condensed financial statements 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 in the appendix. 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

Q1 FY 2017 Statement of Operations

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Consolidated Statements of Operations

(Dollars in thousands, except per share and share amounts)

(Unaudited)

Three Months Ended

September 30,

2016 2015

Net revenues $ 49,800 $ 43,871

Cost of goods sold 9,466 8,771

Gross profit 40,334 35,100

Expenses:

Selling, general and administrative 36,866 41,395

Research and development 5,335 6,941

Total expenses 42,201 48,336

Loss from operations (1,867 ) (13,236 )

Other (income) and expense, net (33 ) 2

Loss before income taxes (1,834 ) (13,238 )

Provision for income taxes 24 23

Net loss $ (1,858 ) $ (13,261 )

Net loss per common share:

Basic and diluted $ (0.06 ) $ (0.41 )

Weighted average common shares used in computation:

Basic and diluted 32,985,081 32,210,874

Q1 FY 2017 Balance Sheet

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Consolidated Balance Sheets

(Dollars in thousands, except per share and share amounts)

(Unaudited)

September 30,

2016

June 30,

2016

ASSETS

Current assets

Cash and cash equivalents $ 58,194 $ 60,638

Accounts receivable, net 24,308 23,128

Inventories 16,887 17,440

Marketable securities 705 684

Prepaid expenses and other current assets 1,998 2,992

Total current assets 102,092 104,882

Property and equipment, net 31,820 32,471

Patents, net 4,352 5,013

Other assets 70 40

Total assets $ 138,334 $ 142,406

LIABILITIES AND STOCKHOLDERS’ EQUITY

Current liabilities

Accounts payable $ 8,763 $ 8,506

Accrued expenses 21,688 26,993

Total current liabilities 30,451 35,499

Long-term liabilities

Other liabilities 4,939 6,010

Total liabilities 35,390 41,509

Commitments and contingencies — —

Common stock, $0.001 par value; authorized 100,000,000 common shares at September

30, 2016 and June 30, 2016; issued and outstanding 33,046,180 at September 30, 2016

and 32,792,497 at June 30, 2016, respectively 33

33

Additional paid in capital 432,119 428,235

Accumulated other comprehensive income 61 40

Accumulated deficit (329,269 ) (327,411 )

Total stockholders’ equity 102,944 100,897

Total liabilities and stockholders’ equity $ 138,334 $ 142,406

Q1 FY 2017 Statement of Cash Flows

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Consolidated Statements of Cash Flows

(Dollars in thousands)

(Unaudited)

Three Months Ended

September 30,

2016 2015

Cash flows from operating activities

Net loss $ (1,858 ) $ (13,261 )

Adjustments to reconcile net loss to net cash used in operations

Depreciation of property and equipment 957 887

Amortization and write-off of patents 807 86

Provision for doubtful accounts 150 175

Stock-based compensation 3,450 4,107

Changes in assets and liabilities

Accounts receivable (1,330 ) 3,791

Inventories 553 (1,480 )

Prepaid expenses and other assets 1,314 1,043

Accounts payable 257 (18 )

Accrued expenses and other liabilities (6,376 ) (166 )

Net cash used in operating activities (2,076 ) (4,836 )

Cash flows from investing activities

Purchases of property and equipment (282 ) (1,847 )

Issuance of convertible note receivable — (350 )

Purchases of marketable securities — (17 )

Costs incurred in connection with patents (170 ) (160 )

Net cash used in investing activities (452 ) (2,374 )

Cash flows from financing activities

Exercise of stock options 84 19

Net cash provided by financing activities 84 19

Net change in cash and cash equivalents (2,444 ) (7,191 )

Cash and cash equivalents

Beginning of period 60,638 83,842

End of period $ 58,194 $ 76,651

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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Investor Contact:Jack Nielsen651-202-4919j.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