Exhibit 99.1

CUBIST PHARMACEUTICALS REPORTS FIRST QUARTER 2013 FINANCIAL RESULTS

·              Total Net Revenues of $229.9 Million, Up 9% Over Q1 2012; U.S. CUBICIN Net Revenues of $202.0 Million, Up 9% Over Q1 2012

·              Non-GAAP Diluted EPS of $0.34; GAAP Diluted EPS of $0.09

·              Non-GAAP Adjusted Operating Income of $42.2 Million; GAAP Operating Income of $9.8 Million

Lexington, Mass., April 18, 2013 — Cubist Pharmaceuticals, Inc. (NASDAQ: CBST) today announced results for the first quarter ended March 31, 2013.  The Company will host a conference call and webcast today at 5:00 p.m. ET (details below).

Financial highlights for the first quarter of 2013 (unaudited)

·                  Total net revenues were up 9% over the same period in 2012. Q1 2013 total net revenues were $229.9 million compared to $211.7 million in Q1 2012.

·                  U.S. CUBICIN® (daptomycin for injection) net product revenues increased 9% to $202.0 million from $184.7 million in Q1 2012. CUBICIN international revenues were $12.4 million compared to $12.7 million in Q1 2012.

·                  Non-GAAP adjusted operating income was $42.2 million compared to $71.5 million in the first quarter of 2012. GAAP operating income was $9.8 million compared to $60.0 million in the first quarter of 2012.

·                  Non-GAAP diluted earnings per share (EPS) was $0.34 compared to $0.55 in the first quarter of 2012.  GAAP diluted EPS was $0.09 compared to $0.45 in the first quarter of 2012.

“As we enter this next chapter for the Company, Cubist continues to deliver solid financial results while driving continued growth,” said Michael Bonney, CEO of Cubist.  “We continue to enhance our leadership team and took several important growth-focused actions during the quarter, including obtaining rights to expand our acute care pipeline through our option agreement with Adynxx and securing the worldwide commercialization rights to our potential blockbuster candidate, ceftolozane/tazobactam. We are making solid progress toward our Building Blocks of Growth and are well-positioned to extend our leadership in the hospital and acute care environment.”

First quarter ENTEREG® (alvimopan) net product revenues were $11.2 million, up 19% compared to $9.4 million in the first quarter of 2012. Service revenues for the Company’s co-promote of DIFICID® (fidaxomicin) for the first quarter were $3.6 million.

As of March 31, 2013, Cubist had $940.7 million in cash, cash equivalents and investments. The total number of Cubist’s common shares outstanding as of March 31, 2013, was 65,163,806.

65 Hayden Avenue, Lexington, MA 02421  P 781.860.8660  F 781.861.0566  www.cubist.com

Updated R&D Expense Guidance

The Company recorded $25.0 million of R&D expense in the first quarter related to the acquisition of certain rights to ceftolozane from Astellas Pharma, Inc.  As a result, the Company updated its R&D expense guidance for 2013 to $400 million - $420 million from the previous estimate of $375 million - $395 million.

Recent Pipeline Highlights

·                  In February, Cubist obtained rights to expand its acute care pipeline by entering into an option agreement with Adynxx, Inc. under which Cubist has the exclusive right to acquire Adynxx following the data readout of Adynxx’s ongoing Phase 2 trial for its lead product candidate, AYX1.  AYX1 targets EGR1, which is a key transcription factor in the establishment of pain that is rapidly induced after painful stimuli or injury.

·                  In February, the U.S. Food and Drug Administration (FDA) designated the Company’s late-stage antibiotic candidate, ceftolozane/tazobactam, as a Qualified Infectious Disease Product (QIDP) for the indications of Hospital-Acquired Bacterial Pneumonia (HABP)/Ventilator-Associated Bacterial Pneumonia (VABP) and Complicated Urinary Tract Infections (cUTI).  Additionally, ceftolozane/tazobactam and surotomycin have been granted Fast Track status in their previously granted QIDP indications, Complicated Intra-Abdominal Infections (cIAI) and Clostridium difficile-associated Diarrhea (CDAD), respectively.

·                  In March, Cubist obtained the rights to ceftolozane in certain Asia-Pacific and Middle East territories from Astellas. With the attainment of these rights, Cubist now owns worldwide rights to develop, manufacture, and commercialize ceftolozane/tazobactam, subject to ongoing milestone and royalty obligations to Astellas.

Recent Corporate Highlights

·                  Michael Tomsicek was promoted to Senior Vice President and Chief Financial Officer. After a decade of leadership at Cubist, David McGirr stepped down as CFO in March. He is serving as Senior Advisor to the CEO and will retire in 2014.

·                  Thomas J. DesRosier joined Cubist as Senior Vice President, Chief Legal Officer, General Counsel and Secretary in March.  He was previously Senior Vice President, General Counsel North America of Sanofi, and was the Chief Legal Officer of Genzyme Corporation prior to the acquisition of Genzyme by Sanofi.

Use of Non-GAAP Financial Measures

Cubist uses non-GAAP financial measures, such as non-GAAP net income, non-GAAP adjusted operating income and non-GAAP diluted EPS, to assess and analyze its operational results and trends and to make financial and operational decisions.  Cubist believes these non-GAAP financial measures are also useful to investors because they provide greater transparency regarding Cubist’s operating performance.  These non-GAAP financial measures should not be considered an alternative to measurements required by GAAP, such as net income, operating income and earnings per share, and should not be considered

measures of Cubist’s liquidity.  In addition, these non-GAAP financial measures are unlikely to be comparable with non-GAAP information provided by other companies.  Reconciliations between non-GAAP financial measures and GAAP financial measures are included in the tables accompanying this press release after the unaudited condensed consolidated financial statements.

***********************CONFERENCE CALL & WEBCAST INFORMATION***********************

CUBIST Q1 2013 FINANCIAL RESULTS

Thursday, April 18, 2013 at 5:00 pm ET

U.S./Canada Attendee Dial-in: (855) 319-7654

International Attendee Dial-in: (484) 756-4327

Attendee Passcode: 27242301

24-HOUR REPLAY U.S./CANADA: (855) 859-2056

24-HOUR REPLAY INTERNATIONAL: (404) 537-3406

Conference ID: 27242301

CALL WILL ALSO BE BROADCAST LIVE, LISTEN ONLY, VIA THE WEB AT:

https://tinyurl.com/CBST1Q13

Attendee Password: 041813

Replay will be available for 90 days at www.cubist.com

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About Cubist

Cubist Pharmaceuticals, Inc. is a biopharmaceutical company focused on the research, development, and commercialization of pharmaceutical products that address significant unmet medical needs in the acute care environment. Cubist is headquartered in Lexington, Mass. Additional information can be found at Cubist’s web site at www.cubist.com.

Cubist Safe Harbor Statement

This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995 and other federal securities laws. Any statements contained herein which do not describe historical facts, including but not limited to, statements regarding: (i) our unaudited first quarter financial results, (ii) our belief in the blockbuster potential of ceftolozane/tazobactam, (iii) the potential for Cubist to acquire Adynxx, and (iv) our Building Blocks of Growth, are forward-looking statements which involve risks and uncertainties that could cause actual results to differ materially from those discussed in such forward-looking statements. Such risks and uncertainties include: the risk that our final first quarter financial results will differ materially from our expected results disclosed in this release; our ability to continue to grow revenues from the sale of CUBICIN and ENTEREG; the ability of our third-party suppliers to produce and deliver adequate amounts of our products and product candidates; the strength of, and our ability to successfully enforce, our intellectual property portfolio protecting our products and product candidates; competition from generic drug companies such as Teva and Hospira; our ability to successfully develop, gain marketing approval for and commercially launch ceftolozane/tazobactam and our other product candidates for their planned indications and on the timelines that we expect; our ability to discover, in-license or acquire new products and product candidates; our ability to achieve

and manage our growth in our business; the potential that the Phase 2 trial for AYX1 will not yield positive results or support further development of AYX1; and those additional factors discussed in our most recent Annual Report on Form 10-K filed with the Securities and Exchange Commission. We caution investors not to place considerable reliance on the forward-looking statements contained in this press release. These forward-looking statements speak only as of the date of this document, and we undertake no obligation to update or revise any of these statements.

Cubist Pharmaceuticals, Inc.

INVESTORS:

Cubist Pharmaceuticals, Inc.

Eileen C. McIntyre, (781) 860-8533

Vice President, Investor Relations

eileen.mcintyre@cubist.com

or

MEDIA:

Julie DiCarlo, (781) 860-8777

Senior Director, Corporate Communications

julie.dicarlo@cubist.com

Tables to follow

CUBIST PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

UNAUDITED

(in thousands)

CUBIST PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF INCOME

UNAUDITED

(in thousands, except share and per share data)

(1) Includes add back of interest expense, debt issuance costs and debt discount amortization on 2.50% notes and 2.25% notes to income, net of tax effect

CUBIST PHARMACEUTICALS, INC.

RECONCILIATION OF GAAP TO NON-GAAP FINANCIAL INFORMATION

UNAUDITED

(in thousands, except share and per share data)

(1) The methodology used to compute the tax adjustments above was revised in Q1 2013 to reflect the tax effect of non-GAAP adjustments and to include material, non-recurring discrete items for the period.  The prior year tax adjustment has been revised to conform to the current quarter’s presentation.

(2) Includes add back of interest expense and debt issuance costs on 2.50% notes to income, net of tax effect

(3) Includes add back of interest expense and debt issuance costs on 2.25% notes and 2.50% notes to income, net of tax effect

CUBIST PHARMACEUTICALS, INC.

RECONCILIATION OF GAAP TO NON-GAAP FINANCIAL INFORMATION

UNAUDITED

(in thousands)

CUBIST PHARMACEUTICALS, INC.

RECONCILIATION OF GAAP TO NON-GAAP FINANCIAL INFORMATION

UNAUDITED

(in thousands, except share and per share data)

(1) Includes add back of interest expense and debt issuance costs on 2.50% notes to income, net of tax effect

(2) Includes add back of interest expense and debt issuance costs on 2.25% notes and 2.50% notes to income, net of tax effect

(3) Weighted average shares issued on full conversion