April 4, 2020

Jeffrey Hatfield
Chief Executive Officer
Zafgen, Inc.
3 Center Plaza, Suite 610
Boston, MA 02108

       Re: Zafgen, Inc.
           Preliminary Proxy Statement on Schedule 14A
           Filed March 6, 2020
           File No. 001-36510

Dear Mr. Hatfield:

       We have reviewed your filing and have the following comments. In some of
our
comments, we may ask you to provide us with information so we may better
understand your
disclosure.

       Please respond to these comments within ten business days by providing
the requested
information or advise us as soon as possible when you will respond. If you do
not believe our
comments apply to your facts and circumstances, please tell us why in your
response.

       After reviewing your response to these comments, we may have additional
comments.

Preliminary proxy statement on Schedule 14A filed March 6, 2020

Summary, page 1

1.    Please place your disclosure of Chondrial's business in appropriate
context by providing
      disclosure of the following:
        Chondrial may need to develop novel clinical endpoints in later stage
clinical trials
           for CTI-1601, as referenced on page 32;
        In GLP toxicology studies of CTI-1601, occasional transient rigidity
immediately
           after dosing in certain non-human primates was observed, as
referenced on page 163;
           and
        Chondrial is dependent upon in-licensed intellectual property for the
development of
           CTI-1601, as discussed on pages 60 to 61 and pages 165 to 166.
 Jeffrey Hatfield
FirstName LastNameJeffrey Hatfield
Zafgen, Inc.
Comapany NameZafgen, Inc.
April 4, 2020
Page 4,
April 2 2020 Page 2
FirstName LastName
The Merger
Background of the Merger, page 74

2.       We note your disclosure that Chondrial submitted a preliminary
non-binding written
         proposal. Please expand your disclosure to explain how the exchange
ratio was
         determined. Address in your disclosure how the Board arrived at the
determination to
         approve the term to increase the Chondrial valuation by $111,656 per
day beginning on
         March 31, 2020 through the closing of the merger.

Chondrial's Business
Overview, page 157

3.       We note your disclosure that Chondrial's additional pipeline products
are in the
         nonclinical stage of development. Please expand your disclosure to
include material terms
         of development programs that are material to Chondrial's business.
Alternatively, please
         remove this disclosure.
Chondrial's Strategy, page 157

4.       Please revise your disclosure to remove any implication that Chondrial
will be successful
         in obtaining regulatory approval for CTI-1601 in an accelerated
manner. As illustrative
         examples only, we note the following disclosures:
           Chondrial is working with the FDA and collaborating with key opinion
leaders to
             develop an efficient clinical development plan for the regulatory
approval of CTI-
             1601.
           Chondrial partners with experts in every aspect of development to
ensure the most
             expeditious development program.
           This expertise, along with the platform technology provides
Chondrial with the
             ability to optimize the development and commercialization of the
drug and biologic
             candidates under development and maximize the near and longer-term
value of the
             Chondrian platform.
In-License Agreements, page 165

5.       Please expand your disclosure to include all material terms of the
License Agreements
         with Wake Forest University Health Sciences and Indiana University,
including aggregate
         potential milestone payments, royalty term, term of the agreement and
termination
         provisions.
Intellectual Property, page 165

6.       Please revise this section to clearly distinguish among owned patents,
licensed patents and
         provisional patent applications, discuss the significance of a
provisional patent application
         versus an issued patent and identify applicable foreign jurisdictions.
 Jeffrey Hatfield
Zafgen, Inc.
April 4, 2020
Page 3

        We remind you that the company and its management are responsible for
the accuracy
and adequacy of their disclosures, notwithstanding any review, comments, action
or absence of
action by the staff.

       You may contact Michael Fay at 202-551-3812 or Vanessa Robertson at
202-551-3649 if
you have questions regarding comments on the financial statements and related
matters. Please
contact Courtney Lindsay at 202-551-7237 or Christine Westbrook at 202-551-5019
with any
other questions.



                                                          Sincerely,
FirstName LastNameJeffrey Hatfield
                                                          Division of
Corporation Finance
Comapany NameZafgen, Inc.
                                                          Office of Life
Sciences
April 4, 2020 Page 3
cc:       Andrew Goodman, Esq.
FirstName LastName