Exhibit 99.1

CARDIOVASCULAR SYSTEMS REPORTS FISCAL 2013

THIRD-QUARTER FINANCIAL RESULTS

Conference Call Scheduled for Today, May 1, 2013, at 3:45 PM CT (4:45 PM ET)

• Revenues of $26.5 million rose 25 percent over the fiscal 2012 third quarter, and 5 percent sequentially over the fiscal 2013 second quarter

• Stealth 360º^® revenues increased to more than 96 percent of total device revenues

• Pivotal 30-day data from ORBIT II coronary study presented at ACC

• Results exceeded trial’s two primary safety and efficacy endpoints by a significant margin

• PMA submission to treat coronary artery disease completed on March 15

• Net proceeds of approximately $38 million raised in public offering of common stock

St. Paul, Minn., May 1, 2013 – Cardiovascular Systems, Inc. (CSI) (Nasdaq: CSII), a medical device company developing and commercializing innovative interventional treatment systems for vascular disease, today reported financial results for its fiscal third quarter ended March 31, 2013.

CSI’s third-quarter revenues rose to $26.5 million, a 25-percent gain from $21.2 million in the third quarter of fiscal 2012. Substantial demand for the company’s Stealth 360º^® peripheral arterial disease (PAD) System drove Stealth 360º revenues to more than 96 percent of total device revenues. Customer reorder revenues remained strong at 96 percent of total revenue.

The fiscal 2013 third-quarter net loss was less than anticipated at $(6.2) million, or $(0.29) per common share, compared to $(4.2) million, or $(0.23) per common share, in the fiscal 2012 third quarter. Net loss includes expense of $(0.5) million, or $(0.02) per common share, from $4.5 million of debt conversions and valuation changes in a related conversion asset. Adjusted EBITDA for the quarter was a loss of $(3.3) million, compared to a loss of $(2.3) million in fiscal 2012. Losses increased from prior-year periods, primarily due to planned investments of approximately $4.1 million to advance the ORBIT II coronary clinical trial and prepare for a coronary market launch, as well as competitive enhancements to sales and marketing, and expansion of medical education programs.

The company’s third-quarter gross profit margin was 76 percent, similar to the year-earlier quarter. The favorable effect of increased production volume was offset by the higher unit cost of the Stealth 360° compared to the predecessor Diamondback 360° device and by investments to ramp-up CSI’s manufacturing facility in Texas for added capacity.

In March 2013, CSI raised approximately $38 million in a public offering of common stock. Proceeds will be primarily used to fund growth investments including coronary launch preparation, international expansion, clinical studies, product portfolio expansion and education programs.

David L. Martin, CSI president and chief executive officer, said, “We continued to achieve significant milestones during the quarter. Our focused sales strategy and educational initiatives drove rapid adoption of our easy-to-use technology with PAD physicians in both hospital and office-based lab settings. This resulted in continued strong quarterly financial results.”

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Martin continued, “We also presented pivotal 30-day data from our ORBIT II study of severely calcified coronary lesions at the 2013 American College of Cardiology, or ACC, conference. CSI’s mission is to be the primary therapy for calcified artery disease. Our compelling ORBIT II study results demonstrate the substantial potential for our orbital atherectomy technology to treat this most challenging, underserved patient population.

“Building on that success, we submitted a premarket approval, or PMA, application to the FDA for our orbital atherectomy system to treat calcified coronary arteries. This marks another major coronary milestone for CSI, as we drive toward this $1.5 billion market opportunity.”

In the first nine months of fiscal 2013, revenues increased to $75.1 million, up 26 percent from the fiscal 2012 nine-month period. Gross margin was comparable to the prior-year period at 77 percent, while operating expenses rose 31 percent due to planned investments similar to those discussed for the third quarter, including approximately $12.6 million for the ORBIT II trial and coronary market preparation. Adjusted EBITDA loss increased by $(3.8) million to $(9.7) million, while the net loss totaled $(17.2) million, or $(0.82) per common share, compared to $(12.2) million, or $(0.69) per common share, in fiscal 2012.

Pivotal ORBIT II Coronary Data Presented at ACC 2013

The Featured Clinical Research session presentation by Dr. Jeffrey Chambers of Metropolitan Heart and Vascular Institute, Minneapolis, demonstrated that CSI’s technology produced clinical outcomes that exceeded the trial’s two primary safety and efficacy endpoints by a significant margin — within one of the most challenging patient populations to treat.

The ORBIT II results showed that at 30 days, patient freedom from major adverse cardiac events, or MACE, was 89.8 percent and procedural success was 89.1 percent (including in-hospital MACE). Patients had less than 50 percent residual stenosis 98.6 percent of the time, and 97.7 percent of stents were successfully delivered.

ORBIT II is evaluating the safety and effectiveness of the company’s orbital atherectomy technology in treating a problematic subset of patients with severely calcified coronary lesions and is the first IDE study in history to seek approval for treating these lesions.

CSI Completes PMA Submission to Treat Coronary Artery Disease

CSI completed submission of its PMA application to the FDA for its orbital atherectomy system, to treat calcified coronary arteries, on March 15, 2013. The FDA agreed to a modular PMA process that allowed CSI to submit the first two modules covering preclinical data and manufacturing/quality systems, while still collecting, compiling and analyzing the clinical data. CSI has now submitted the third and final PMA application module, as well as responses to FDA comments on the first two modules, which were submitted in late 2012.

Fiscal 2013 Fourth-Quarter Outlook

For the fiscal 2013 fourth quarter ending June 30, 2013, CSI anticipates:

• Revenue growth of 17 percent to 21 percent over the fourth quarter of fiscal 2012, to a range of $26.7 million to $27.7 million;

• Gross profit as a percentage of revenues similar to the third quarter of fiscal 2013;

• Operating expenses 7 percent to 8 percent higher than the third quarter of fiscal 2013, including approximately $4.5 million for the ORBIT II trial and preparation for a potential coronary market launch in the future;

• Interest and other expense of approximately $(325,000), excluding the potential effect of debt conversions or valuation changes of the related conversion option asset; and

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• Net loss in the range of $(6.8) million to $(7.4) million, or loss per common share ranging from $(0.28) to $(0.31), assuming 24.2 million average shares outstanding, and excluding the potential effect of debt conversions or valuation changes of the related conversion option asset.

Martin added, “We continue to make growth investments in preparation for a coronary launch, as well as in clinical studies and education programs to further drive PAD adoption. Investing in these opportunities will help us realize the full potential of our technology, support ongoing attractive revenue growth and lead us to profitability over the long term.”

Conference Call Today at 3:45 p.m. CT (4:45 p.m.ET)

Cardiovascular Systems, Inc. will host a live conference call and webcast of its fiscal third-quarter results today, May 1, 2013, at 3:45 p.m. CT (4:45 p.m. ET). To access the call, dial (888) 713-4205 and enter access number 48810662. Please dial in at least 10 minutes prior to the call and wait for assistance, or dial “0” for the operator. To listen to the live webcast, go to the investor information section of the company’s website, www.csi360.com, and click on the webcast icon. A webcast replay will be available beginning at 7 p.m. CT the same day.

For an audio replay of the conference call, dial (888) 286-8010 and enter access number 46269911. The audio replay will be available beginning at 5:45 p.m. CT on Wednesday, May 1, 2013, through 11 p.m. CT on Wednesday, May 8, 2013.

Use of Non-GAAP Financial Measures

To supplement CSI’s consolidated condensed financial statements prepared in accordance with U.S. generally accepted accounting principles (GAAP), CSI uses certain non-GAAP financial measures in this release. Reconciliations of the non-GAAP financial measures used in this release to the most comparable U.S. GAAP measures for the respective periods can be found in tables later in this release immediately following the consolidated statements of operations. Non-GAAP financial measures have limitations as analytical tools and should not be considered in isolation or as a substitute for CSI’s financial results prepared in accordance with GAAP.

About Peripheral Arterial Disease

As many as 12 million Americans, most over age 65, suffer from PAD, which is caused by the accumulation of plaque in peripheral arteries (commonly the pelvis or leg) reducing blood flow. Symptoms include leg pain when walking or at rest. Left untreated, PAD can lead to severe pain, immobility, non-healing wounds and eventually limb amputation. With risk factors such as diabetes and obesity on the rise, the prevalence of PAD is growing at double-digit rates.

Millions of patients with PAD may benefit from treatment with orbital atherectomy utilizing the Stealth 360° and Diamondback 360°, minimally invasive catheter systems developed and manufactured by CSI. These systems use a diamond-coated crown, attached to an orbiting shaft, which sands away plaque while preserving healthy vessel tissue — a critical factor in preventing reoccurrences. Balloon angioplasty and stents have significant shortcomings in treating hard, calcified lesions. Stents are prone to fractures and high recurrence rates, and treatment of hard, calcified lesions often leads to vessel damage and suboptimal results.

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About Cardiovascular Systems, Inc.

Cardiovascular Systems, Inc., based in St. Paul, Minn., is a medical device company focused on developing and commercializing innovative solutions for treating vascular and coronary disease. The company’s Orbital Atherectomy Systems treat calcified and fibrotic plaque in arterial vessels throughout the leg in a few minutes of treatment time, and address many of the limitations associated with existing surgical, catheter and pharmacological treatment alternatives. The U.S. FDA granted 510(k) clearance for the use of the Diamondback Orbital Atherectomy System in August 2007. To date, nearly 110,000 of CSI’s devices have been sold to leading institutions across the United States. CSI has also completed its ORBIT II Investigational Device Exemption clinical trial to evaluate the safety and effectiveness of its orbital technology in treating coronary arteries. The coronary system is limited by federal law to investigational use and is currently not commercially available in the United States.

For more information, visit the company’s website at www.csi360.com.

Safe Harbor

Certain statements in this news release 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. For example, statements in this press release regarding (i) CSI’s potential coronary application; (ii) CSI’s ORBIT II trial; (iii) the anticipated use of proceeds from the public offering of common stock in March 2013; (iv) the $1.5 billion estimate of the market for a coronary application; (v) the potential growth and profitability driven by CSI’s anticipated investments; and (vi) anticipated revenue, gross profit, operating expenses, interest and other expense, and net loss, are forward-looking statements.

These statements involve risks and uncertainties which could cause results to differ materially from those projected, including but not limited to dependence on market growth; the reluctance of physicians to accept new products; the effectiveness of the Stealth 360º; actual clinical trial results; the impact of competitive products and pricing; the difficulty to successfully manage operating costs; fluctuations in quarterly results; FDA clearances and approvals; approval of products for reimbursement and the level of reimbursement; general economic conditions and other factors detailed from time to time in CSI’s SEC reports, including its most recent annual report on Form 10-K and subsequent quarterly reports on Form 10-Q. CSI encourages you to consider all of these risks, uncertainties and other factors carefully in evaluating the forward-looking statements contained in this release. 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 contained in this release. The forward-looking statements made in this release are made only as of the date of this release, and CSI undertakes no obligation to update them to reflect subsequent events or circumstances.

Product Disclosure

The Stealth 360º^® PAD System, Diamondback 360^® PAD System and Predator 360^® PAD System 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 are contraindicated 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.

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Cardiovascular Systems, Inc.

Consolidated Statements of Operations

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

(unaudited)

	Three Months Ended March 31,						Nine Months Ended March 31,
	2013			2012			2013			2012
Revenues	$	26,474		$	21,205		$	75,076		$	59,583
Cost of goods sold		6,241			5,132			17,453			14,038
Gross profit		20,233			16,073			57,623			45,545
Selling, general and administrative		21,650			16,809			62,091			47,892
Research and development		3,993			2,985			11,270			8,133
Total expenses		25,643			19,794			73,361			56,025
Loss from operations		(5,410	)		(3,721	)		(15,738	)		(10,480	)
Interest and other (expense) income		(809	)		(470	)		(1,458	)		(1,705	)
Net loss	$	(6,219	)	$	(4,191	)	$	(17,196	)	$	(12,185	)
Net loss per common share:
Basic and diluted	$	(0.29	)	$	(0.23	)	$	(0.82	)	$	(0.69	)
Weighted average common shares used in computation:
Basic and diluted		21,488,879			17,977,819			20,857,124			17,746,558

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Cardiovascular Systems, Inc.

Consolidated Balance Sheets

(Dollars in Thousands)

(unaudited)

	March 31, 2013		June 30, 2012
ASSETS
Current assets
Cash and cash equivalents	$	69,932	$	35,529
Accounts receivable, net		15,187		13,644
Inventories		6,796		7,061
Prepaid expenses and other current assets		778		1,536
Total current assets		92,693		57,770
Property and equipment, net		2,532		2,163
Patents, net		3,066		2,635
Other assets		742		556
Total assets	$	99,033	$	63,124
LIABILITIES AND STOCKHOLDERS’ EQUITY
Current liabilities
Current maturities of long-term debt	$	4,928	$	4,678
Accounts payable		6,183		5,610
Deferred grant incentive		176		302
Accrued expenses		8,668		7,262
Total current liabilities		19,955		17,852
Long-term liabilities
Long-term debt, net of current maturities		8,851		12,842
Other liabilities		242		241
Total long-term liabilities		9,093		13,083
Total liabilities		29,048		30,935
Commitments and contingencies
Total stockholders’ equity		69,985		32,189
Total liabilities and stockholders’ equity	$	99,033	$	63,124

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Cardiovascular Systems, Inc.

Supplemental Sales Information

(Dollars in Thousands)

(unaudited)

	Three months ended March 31,						Nine months ended March 31,
	2013			2012			2013			2012
Device revenue	$	23,135		$	18,800		$	65,863		$	52,842
Other product revenue		3,339			2,405			9,213			6,741
Total revenue	$	26,474		$	21,205		$	75,076		$	59,583
Device units sold		7,314			5,894			20,810			16,689
New customers		50			41			132			123
Reorder revenue %		96	%		96	%		97	%		95	%

Non-GAAP Financial Measures

To 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 release.

Reconciliations of Adjusted EBITDA to the most comparable U.S. GAAP measure for the respective periods can be found in the table below. 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 is included following the reconciliation table below.

Cardiovascular Systems, Inc.

Adjusted EBITDA

(Dollars in Thousands)

(unaudited)

	Actual
	Three Months  Ended March 31,						Nine Months Ended March 31,
	2013			2012			2013			2012
Loss from operations	$	(5,410	)	$	(3,721	)	$	(15,738	)	$	(10,480	)
Add: Stock-based compensation		1,876			1,200			5,316			3,919
Add: Depreciation and amortization		241			228			688			676
Adjusted EBITDA	$	(3,293	)	$	(2,293	)	$	(9,734	)	$	(5,885	)

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Use and Economic Substance of Non-GAAP Financial Measures Used by CSI and Usefulness of Such Non-GAAP Financial Measures to Investors

CSI uses Adjusted EBITDA as a supplemental measure of performance and believes this measure facilitates operating performance comparisons from period to period and company to company by factoring out potential differences caused by depreciation and amortization expense and non-cash charges such as stock based compensation. CSI’s management uses Adjusted EBITDA to analyze the underlying trends in CSI’s business, assess the performance of CSI’s core operations, establish operational goals and forecasts that are used to allocate resources and evaluate CSI’s performance period over period and in relation to its competitors’ operating results. Additionally, CSI’s management is evaluated on the basis of Adjusted EBITDA when determining achievement of their incentive compensation performance targets.

CSI believes that presenting Adjusted EBITDA provides investors greater transparency to the information used by CSI’s management for its financial and operational decision-making and allows investors to see CSI’s results “through the eyes” of management. CSI also believes that providing this information better enables CSI’s investors to understand CSI’s operating performance and evaluate the methodology used by CSI’s management to evaluate and measure such performance.

The following is an explanation of each of the items that management excluded from Adjusted EBITDA and the reasons for excluding each of these individual items:

• Stock-based compensation. CSI excludes stock-based compensation expense from its non-GAAP financial measures primarily because such expense, while constituting an ongoing and recurring expense, is not an expense that requires cash settlement. CSI’s management also believes that excluding this item from CSI’s non-GAAP results is useful to investors to understand the application of stock-based compensation guidance and its impact on CSI’s operational performance, liquidity and its ability to make additional investments in the company, and it allows for greater transparency to certain line items in CSI’s financial statements.

• Depreciation and amortization expense. CSI excludes depreciation and amortization expense from its non-GAAP financial measures primarily because such expenses, while constituting ongoing and recurring expenses, are not expenses that require cash settlement and are not used by CSI’s management to assess the core profitability of CSI’s business operations. CSI’s management also believes that excluding these items from CSI’s non-GAAP results is useful to investors to understand CSI’s operational performance, liquidity and its ability to make additional investments in the company.

Material Limitations Associated with the Use of Non-GAAP Financial Measures and Manner in which CSI Compensates for these Limitations

Non-GAAP financial measures have limitations as analytical tools and should not be considered in isolation or as a substitute for CSI’s financial results prepared in accordance with GAAP. Some of the limitations associated with CSI’s use of these non-GAAP financial measures are:

• Items such as stock-based compensation do not directly affect CSI’s cash flow position; however, such items reflect economic costs to CSI and are not reflected in CSI’s “Adjusted EBITDA” and therefore these non-GAAP measures do not reflect the full economic effect of these items.

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• Non-GAAP financial measures are not based on any comprehensive set of accounting rules or principles and therefore other companies may calculate similarly titled non-GAAP financial measures differently than CSI, limiting the usefulness of those measures for comparative purposes.

• CSI’s management exercises judgment in determining which types of charges or other items should be excluded from the non-GAAP financial measures CSI uses.

CSI compensates for these limitations by relying primarily upon its GAAP results and using non-GAAP financial measures only supplementally. CSI provides full disclosure of each non-GAAP financial measure CSI uses and detailed reconciliations of each non-GAAP measure to its most directly comparable GAAP measure. CSI encourages investors to review these reconciliations. CSI qualifies its use of non-GAAP financial measures with cautionary statements as set forth above.

Contacts:

Cardiovascular Systems, Inc. Investor Relations (651) 259-2800 investorrelations@csi360.com Padilla Speer Beardsley Inc. Marian Briggs (612) 455-1742 mbriggs@padillaspeer.com   Matt Sullivan (612) 455-1709 msullivan@padillaspeer.com

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