Exhibit 32.1

CERTIFICATION PURSUANT TO 18 U.S.C. §1350

In connection with the Quarterly Report on Form 10-Q of Eleven Biotherapeutics, Inc. (the “Company”) for the fiscal quarter ended September 30, 2014 as filed with the Securities and Exchange Commission on the date hereof (the “Report”), the undersigned hereby certify, pursuant to 18 U.S.C. Section 1350, that, to the best of their knowledge:

(1) the Report fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended; and

(2) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

/s/    Abbie C. Celniker        

Abbie C. Celniker

President and Chief Executive Officer

(Principal Executive Officer)

Dated: November 13, 2014

/s/    Gregory D. Perry        

Gregory D. Perry

Chief Financial and Business Officer

(Principal Financial Officer)

Dated: November 13, 2014