Exhibit 16.1

January 8, 2015

Securities and Exchange Commission

100 F Street, N.E.

Washington, DC 20549

Commissioners:

We have read the statements made by Zafgen, Inc. under the heading “Change in Accounting Firm Relationships”, in this registration statement on Form S-1 and we agree with the statements concerning our Firm under that heading.

Very truly yours,

/s/ Edelstein and Company LLP

Edelstein and Company LLP

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