Third Quarter 2009 Highlights:

3Q09 Total net revenues up 28% vs. 3Q08

3Q09 Total net revenues up 10% vs. 2Q09

3Q09 GAAP EPS of 42 cents

3Q09 non-GAAP EPS of 65 cents

With three quarters of 2009 revenue recorded, Cubist has tightened its full year 2009 guidance for CUBICIN U.S. net revenue to between $520 and $525 Million, which is within the range the company announced in January. Cubist's updated guidance for the full year would represent CUBICIN U.S. net revenue growth of at least 25%.

"Today we have reported another strong quarter", said Michael Bonney, President and CEO of Cubist. "We continue to make great progress toward our goal of building the world's leading company focusing on therapies for acutely ill patients. Our strong top and bottom line results have been achieved in an environment that has been tough for many branded pharmaceuticals. Cubist's top line performance reflects the unique strengths of our anti-MRSA agent CUBICIN as well as the expertise of our acute care medical and commercial organizations. Our four development programs and candidates are all progressing toward important data and decision points in the next 3 to 9 months."

Net Income

Net income for the third quarter ended September 30, 2009, on a GAAP basis, was $25.4 million, or $0.44 and $0.42 per basic and diluted share, respectively, as compared to net income of $25.0 million, or $0.44 per basic and diluted share for the third quarter ended September 30, 2008.

Cubist's non-GAAP net income for the third quarter ended September 30, 2009 was $43.2 million, or $0.75 and $0.65 per basic and diluted share, respectively, as compared to non-GAAP net income of $31.1 million, or $0.55 and $0.48 per basic and diluted share, respectively, for the third quarter ended September 30, 2008. A reconciliation between GAAP and non-GAAP net income is provided in the Condensed Consolidated Statement of Operations Non-GAAP table included with this release.

As of September 30, 2009, Cubist had $519.8 million in cash, cash equivalents and investments. The total number of Cubist's common shares outstanding as of September 30, 2009 was 57,912,625.

Pipeline Update

RSV Co-development program with Alnylam:

In collaboration with Alnylam, Cubist is in the final stages of evaluating all data for RSV-01 and second generation candidates. The co-development partners will determine next steps in a path forward for development of a potential RSV therapy in pediatrics as well as in adults by year end.

Two antibiotic candidates now in Phase 1

In the first half of 2010 Cubist anticipates making important Phase 2 decisions on our two antibiotic candidates now in Phase 1 studies”an IV antibiotic in development for the treatment of infections caused by multi-drug-resistant Gram-negative infections and an oral antibiotic in development as treatment for clostridium difficile associated diarrhea, or CDAD. Key input for these decisions will be safety data from the Phase 1 single- and multiple-ascending dose studies which should be available the first half of next year.

Ecallantide, Phase 2 trials proceeding smoothly

During 2010 Cubist anticipates a number of important milestones for the company's Phase 2 candidate, ecallantide, in-licensed from Dyax last year and being developed by Cubist for the reduction of blood loss during on-pump cardiac surgery. Earlier this year, Cubist initiated both CONSERV 1 in the U.S. and CONSERV 2 in the EU. Enrollment is proceeding smoothly. The company anticipates that data from these trials will be unblinded early in 2010 with preparation to follow for end-of-Phase 2 meetings with the U.S. and EU regulatory bodies.

Use of Non-GAAP Financial Measures

Cubist uses non-GAAP net income and non-GAAP net income per share data to improve its analysis of operational results and trends. Cubist's management also uses these non-GAAP figures to make financial and operational decisions as these numbers exclude non-operational activities and because management believes these measures are useful to investors because they provide greater transparency regarding Cubist's operating performance. These measures should not be considered an alternative to measurements required by GAAP, such as net income and net income per share, and should not be considered measures of our liquidity. In addition, these non-GAAP measures are unlikely to be comparable with non-GAAP information provided by other companies. A reconciliation 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 and Webcast Information

Teleconference Information: Event Date: 10/15/2009 Event Time: 5:00 PM Eastern Event Title: Third Quarter 2009 Earnings Call Participant Dial-In Numbers: 877-407-8289 For more information: http://www.investorcalendar.com/IC/CEPage.asp?ID=149453 Replay / archive access is here: (877) 660-6853 (Toll free) (201) 612-7415 (Local / Int'l) Acct. #: 351 Conference ID: 332096

About Cubist

Cubist Pharmaceuticals, Inc. is a biopharmaceutical company focused on the research, development, and commercialization of pharmaceutical products that address unmet medical needs in acutely ill patients. In the U.S., Cubist markets CUBICIN® (daptomycin for injection), the first antibiotic in a new class of anti-infectives called lipopeptides. In July 2008, Cubist entered into an agreement with AstraZeneca to promote their established antibiotic, MERREM® I.V. (meropenem for injection) in the U.S. The Cubist product pipeline includes ecallantide, a recombinant human protein in Phase 2 clinical trials ” CONSERV-1 and CONSERV-2 ” for the reduction of blood loss during on pump cardiac surgery, and two Phase 1 programs that address unmet medical needs, one in CDAD (Clostridium difficile-associated diarrhea) and the other in multi-drug resistant (MDR) Gram-negative infections. In addition, the Company, in collaboration with Alnylam Pharmaceuticals, Inc. (Cambridge, MA), has a pre-IND and a Phase 2 program underway for novel treatments for respiratory syncytial virus infections using Alnylam's RNA-interference technology. Cubist is headquartered in Lexington, MA. 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 regarding CUBICIN performance and our pipeline programs. There are many factors that could cause actual results to differ materially from those in these forward-looking statements. These factors include the following: the level of acceptance of CUBICIN by physicians, patients, third-party payors and the medical community; any changes in the current or anticipated market demand or medical need for CUBICIN; any unexpected adverse events related to CUBICIN, particularly as CUBICIN is used in the treatment of a growing number of patients around the world; the results of the patent infringement lawsuit that Cubist has filed against Teva Parenteral Medicines, Inc. and its affiliates in response to Teva's Abbreviated New Drug Application, or ANDA, with the U.S.