Zafgen Reports Second Quarter 2018 Operating and Financial Results Phase 1 clinical trial for ZGN-1258 for Prader-Willi syndrome (PWS) expected to begin in the fourth quarter 2018 Multiple ZGN-1258 nonclinical studies ac

Zafgen Reports Second Quarter 2018 Operating and Financial Results

Phase 1 clinical trial for ZGN-1258 for Prader-Willi syndrome (PWS) expected to begin in the fourth

Multiple ZGN-1258 nonclinical studies accepted for presentation at upcoming

Foundation for Prader-Willi Research (FPWR) Annual Conference

Initiated 1.8 mg dosing arm in

ZGN-1061 Phase 2 clinical trial for type 2 diabetes; results from additional arm expected early 2019

Company to host conference call today at 4:30 PM ET

Boston, Mass., August 7, 2018 Zafgen, Inc. (Nasdaq:ZFGN), a clinical-stage biopharmaceutical company leveraging its

proprietary knowledge of MetAP2 systems biology to develop novel therapies for patients affected by a range of metabolic diseases, today reported its second quarter 2018 financial results.

2018 is an important year of execution on our plan for our novel second-generation MetAP2 pipeline, said Jeffrey Hatfield, Chief Executive

Officer. We ve continued to make significant progress this year, highlighted by positive data from the initial part of our Phase 2 clinical trial of ZGN-1061 in patients with type 2 diabetes, launch

of the natural history study of PWS, advancement towards clinical testing for ZGN-1258, strengthening of our balance sheet, and key personnel additions. We expect this progress to continue throughout the

remainder of 2018 and beyond, with near-term milestones for all of our key pipeline programs.

Recent Corporate and Program Highlights

Second Quarter 2018 Financial Results

The completion of our recent public offering of common stock has provided the Company with additional capital to advance the Company s

pipeline through multiple value-creating milestones, said Patricia Allen, Chief Financial Officer. We ended the quarter with $75.8 million of cash, cash equivalents and marketable securities and raised net proceeds of approximately

$64.6 million from our recent public offering which closed in early July 2018.

Cash, Cash Equivalents and Marketable Securities

As of June 30, 2018, the Company had cash, cash equivalents and marketable securities totaling $75.8 million. In July 2018, the Company

completed an underwritten public offering of its common stock, which included the full exercise of the underwriters option to purchase additional shares, resulting in net proceeds of approximately $64.6 million. After giving effect to the

estimated net proceeds from the Company s public offering of common stock, the unaudited pro forma cash, cash equivalents and marketable securities balance was $140.4 million as of June 30, 2018.

The Company reported a net loss for the second quarter of 2018 of $15.8 million, or $0.57 per share, compared to a net loss of $13.3 million, or

$0.49 per share, for the second quarter of 2017.

The weighted average common shares (basic and diluted) outstanding used to compute net loss per share

were 27,565,064 for the second quarter of 2018 compared to 27,407,408 for the same quarter of 2017.

Research and Development Expenses

Research and development expenses for the second quarter of 2018 were $12.2 million compared to $10.5 million for the second quarter of 2017. The

increase in research and development expenses compared to the prior year period was primarily due to increased costs related to the ZGN-1258 program as IND enabling studies progressed during the quarter as the

program advances towards the filing of an IND. The increase in research and development expenses was also the result of increased costs associated with the ongoing Phase 2 clinical trial for ZGN-1061. There

were also increases in personnel related costs and non-cash stock-based compensation expense in the second quarter of 2018 as compared to the second quarter of 2017. These increases in research and development

costs were partially offset by a decrease in nonclinical and manufacturing costs associated with our ZGN-1061 program.

General and Administrative Expenses

administrative expenses for the second quarter of 2018 were $3.4 million, compared to $3.0 million for the second quarter of 2017. The increase in general and administrative expenses as compared to the prior year period was primarily due

to an increase in personnel related costs as well as an increase in professional fees primarily related to multi-country patent filing costs, partially offset by a decrease in non-cash stock-based compensation

2018 Financial Guidance

expects that its cash, cash equivalents and marketable securities balance will be greater than $100 million as of December 31, 2018.

Conference Call Information

Zafgen will host an investor

conference call today, August 7, 2018 at 4:30 p.m., Eastern Time, to discuss the Company s second quarter 2018 results as well as other forward-looking information about Zafgen s business. Investors and other interested parties may

participate by dialing (844) 824-7428 in the United States or (973) 500-2177 outside the United States and referencing conference ID number 9168629. The call will also

be webcast live on the Company s website at https://zafgen.gcs-web.com/events-and-presentations. A replay of this conference

call will be available beginning at 7:30 p.m. ET on August 7, 2018 through August 14, 2018 by dialing (855) 859-2056 in the United States or (404) 537-3406

outside the United States. To access the replay please provide Conference ID number 9168629.

Zafgen (Nasdaq:ZFGN) is a clinical-stage biopharmaceutical company leveraging its proprietary MetAP2 biology platform to develop novel therapies for patients

affected by complex metabolic diseases. Zafgen has pioneered the study of MetAP2 inhibitors in both common and rare metabolic disorders and is currently advancing programs for type 2 diabetes, Prader-Willi syndrome and liver diseases. The

Company s lead product candidate, ZGN-1061, a MetAP2 inhibitor for difficult-to-control type 2 diabetes, has successfully

completed the initial part of a Phase 2 clinical trial. Learn more at www.zafgen.com.

Safe Harbor Statement

Various statements in this release concerning Zafgen s future expectations, plans and prospects, including without limitation, Zafgen s expectations

regarding the development and use of ZGN-1258, ZGN-1061 and other second-generation MetAP2 inhibitors as treatments for metabolic diseases including Prader-Willi

syndrome, type 2 diabetes and obesity and Zafgen s expectations with respect to the timing and success of its nonclinical studies and clinical trials of ZGN-1258,

ZGN-1061 and its other product candidates, Zafgen s expected cash, cash equivalents and marketable securities balance as of December 31, 2018, and Zafgen s expectations regarding the length of

its cash runway, may constitute forward-looking statements for the purposes of the safe harbor provisions under The Private Securities Litigation Reform Act of 1995 and other federal securities laws. Forward-looking statements can be identified by

terminology such as anticipate, believe, could, could increase the likelihood, estimate, expect, intend, is planned, may, should,

will, will enable, would be expected, look forward, may provide, would or similar terms, variations of such terms or the negative of those terms. Actual results may differ

materially from those indicated by these forward-looking statements as a result of various important factors, including, without limitation, Zafgen s ability to successfully demonstrate the efficacy and safety of

ZGN-1258, ZGN-1061 and its other product candidates and to differentiate ZGN-1258,

ZGN-1061 and its other product candidates from first-generation MetAP2 inhibitors, such as beloranib, the nonclinical and clinical results for ZGN-1258, ZGN-1061 and its other product candidates, which may not support further development and marketing approval, actions of regulatory agencies, which may affect the initiation, timing and progress of nonclinical

studies and clinical trials of its product candidates, Zafgen s ability to obtain, maintain and protect its intellectual property, Zafgen s ability to enforce its patents against infringers and defend its patent portfolio against

challenges from third parties, competition from others developing products for similar uses, Zafgen s ability to manage operating expenses, Zafgen s ability to obtain additional funding to support its business activities and establish and

maintain strategic business alliances and new business initiatives when needed, Zafgen s ability to attract and retain personnel, Zafgen s dependence on third parties for development, manufacture, marketing, sales and distribution of

product candidates, and unexpected expenditures, as well as those risks more fully discussed in the section entitled Risk Factors in Zafgen s most recent Annual Report on Form 10-K filed with

the Securities and Exchange Commission, as well as discussions of potential risks, uncertainties, and other important factors in Zafgen s subsequent filings with the Securities and Exchange Commission. In addition, any forward-looking

statements represent Zafgen s views only as of today and should not be relied upon as representing its views as of any subsequent date. Zafgen explicitly disclaims any obligation to update any forward-looking statements, whether as a result of

new information, future events or otherwise.

Media/Investor Relations Contacts:

Chief Financial Officer

Ten Bridge Communications

Condensed Consolidated Statements of Operations

(In thousands, except share and per share data)

Condensed Consolidated Balance Sheets

(In thousands, except share and per share data)