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Document and Entity Information - shares	6 Months Ended
Document and Entity Information - shares	Jun. 30, 2017	Jul. 31, 2017
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Jun. 30, 2017
Document Fiscal Year Focus	2017
Document Fiscal Period Focus	Q2
Trading Symbol	ZFGN
Entity Registrant Name	Zafgen, Inc.
Entity Central Index Key	0001374690
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		27,483,925

Condensed Consolidated Balance Sheets (Unaudited) - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 31,726	$ 32,352
Marketable securities	74,266	96,842
Tax incentive receivable	368	347
Prepaid expenses and other current assets	1,605	1,358
Total current assets	107,965	130,899
Tax incentive receivable	234
Property and equipment, net	588	661
Other assets	58	61
Total assets	108,845	131,621
Current liabilities:
Accounts payable	4,447	2,572
Accrued expenses	2,709	3,733
Notes payable, current	2,063	3,589
Total current liabilities	9,219	9,894
Total liabilities	9,219	9,894
Commitments and contingencies (Note 7)
Stockholders' equity:
Preferred stock; $0.001 par value per share; 5,000,000 shares authorized as of June 30, 2017 and December 31, 2016; no shares issued and outstanding as of June 30, 2017 and December 31, 2016
Common stock, $0.001 par value per share; 115,000,000 shares authorized as of June 30, 2017 and December 31, 2016; 27,449,465 and 27,332,551 shares issued and outstanding as of June 30, 2017 and December 31, 2016, respectively	27	27
Additional paid-in capital	363,547	359,329
Accumulated deficit	(263,907)	(237,549)
Accumulated other comprehensive loss	(41)	(80)
Total stockholders' equity	99,626	121,727
Total liabilities and stockholders' equity	$ 108,845	$ 131,621

Condensed Consolidated Balance Sheets (Unaudited) (Parenthetical) - $ / shares	Jun. 30, 2017	Dec. 31, 2016
Statement of Financial Position [Abstract]
Preferred stock, par value per share	$ 0.001	$ 0.001
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value per share	$ 0.001	$ 0.001
Common stock, shares authorized	115,000,000	115,000,000
Common stock, shares issued	27,449,465	27,332,551
Common stock, shares outstanding	27,449,465	27,332,551

Condensed Consolidated Statements of Operations and Comprehensive Loss (Unaudited) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Income Statement [Abstract]
Revenue	$ 0	$ 0	$ 0	$ 0
Operating expenses:
Research and development	10,528	10,163	20,205	22,660
General and administrative	3,008	4,899	6,596	10,259
Total operating expenses	13,536	15,062	26,801	32,919
Loss from operations	(13,536)	(15,062)	(26,801)	(32,919)
Other income (expense):
Interest income	247	225	474	434
Interest expense	(53)	(140)	(126)	(300)
Foreign currency transaction gains (losses), net	(5)	(51)	95	21
Total other income (expense), net	189	34	443	155
Net loss	$ (13,347)	$ (15,028)	$ (26,358)	$ (32,764)
Net loss per share, basic and diluted	$ (0.49)	$ (0.55)	$ (0.96)	$ (1.20)
Weighted average common shares outstanding, basic and diluted	27,407,408	27,272,225	27,379,122	27,267,830
Comprehensive loss:
Net loss	$ (13,347)	$ (15,028)	$ (26,358)	$ (32,764)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities	22	(15)	39	193
Total other comprehensive income (loss)	22	(15)	39	193
Total comprehensive loss	$ (13,325)	$ (15,043)	$ (26,319)	$ (32,571)

Condensed Consolidated Statements of Cash Flows (Unaudited) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016
Cash flows from operating activities:
Net loss	$ (26,358)	$ (32,764)
Adjustments to reconcile net loss to net cash used in operating activities
Stock-based compensation expense	4,103	5,610
Non-cash interest expense	10	24
Depreciation expense	89	102
Unrealized foreign currency transaction gains	(21)	(108)
Premium on marketable securities, net	(224)	(233)
Amortization of premium on marketable securities	145	715
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	(247)	374
Tax incentive receivable	(234)	(250)
Accounts payable	1,875	(4,710)
Accrued expenses	(998)	(1,039)
Net cash used in operating activities	(21,860)	(32,279)
Cash flows from investing activities:
Proceeds from sales and maturities of marketable securities	79,994	88,660
Purchases of marketable securities	(57,300)	(69,907)
Purchases of property and equipment	(16)	(660)
Net cash provided by investing activities	22,678	18,093
Cash flows from financing activities:
Repayments of notes payable	(1,559)	(1,438)
Proceeds from exercise of common stock options and employee stock purchase plan	115	55
Net cash used in financing activities	(1,444)	(1,383)
Net decrease in cash and cash equivalents	(626)	(15,569)
Cash and cash equivalents at beginning of period	32,352	35,595
Cash and cash equivalents at end of period	31,726	20,026
Supplemental disclosure of non-cash investing and financing activities:
Property and equipment included in accounts payable		204
Supplemental disclosure of cash flow information:
Cash paid for interest	$ 103	$ 224

Nature of the Business and Basis of Presentation	6 Months Ended
Nature of the Business and Basis of Presentation	Jun. 30, 2017
Accounting Policies [Abstract]
Nature of the Business and Basis of Presentation	1. Nature of the Business and Basis of Presentation Zafgen, Inc., or the Company, was incorporated on November 22, 2005 under the laws of the State of Delaware. The Company is a biopharmaceutical company dedicated to significantly improving the health and well-being of patients affected by metabolic diseases including type 2 diabetes and obesity. The Company is focused on developing novel therapeutics that treat the underlying biological mechanisms through the methionine aminopeptidase 2 (“MetAP2”) pathway. The Company has pioneered the study of MetAP2 inhibitors in both common and rare forms of obesity. The Company’s lead product candidate is ZGN-1061, a novel fumagillin-class MetAP2 inhibitor administered by subcutaneous injection, which is currently being profiled for its utility in the treatment of metabolic diseases including type 2 diabetes and obesity. Since its inception, the Company has devoted substantially all of its efforts to research and development, recruiting management, acquiring operating assets and raising capital. Currently, the Company is focusing its personnel and financial resources on ZGN-1061 and the discovery of novel and highly differentiated MetAP2 inhibitors. The Company is subject to risks common to companies in the biotechnology industry including, but not limited to, new technological innovations, protection of proprietary technology, dependence on key personnel, compliance with government regulations and the need to obtain additional financing. Product candidates currently under development will require significant additional research and development efforts, including extensive pre-clinical and clinical testing and regulatory approval, prior to commercialization. These efforts require significant amounts of additional capital, adequate personnel infrastructure, and extensive compliance-reporting capabilities. The Company’s product candidates are all in the research and development stage. There can be no assurance that the Company’s research and development will be successfully completed, that adequate protection for the Company’s intellectual property will be obtained, that any product candidates developed will obtain necessary government regulatory approval or that any approved products will be commercially viable. Even if the Company’s product development efforts are successful, it is uncertain when, if ever, the Company will generate significant revenue from product sales. The Company operates in an environment of rapid change in technology and substantial competition from pharmaceutical and biotechnology companies. In addition, the Company is dependent upon the services of its employees and consultants. The Company has incurred losses and negative cash flows from operations since its inception. As of June 30, 2017, the Company had an accumulated deficit of $263.9 million. From its inception through June 30, 2017, the Company received net proceeds of $333.3 million from the sales of redeemable convertible preferred stock, the issuance of convertible promissory notes, the proceeds from its initial public offering (“IPO”) in June 2014 and its follow-on offering in January 2015. Until such time, if ever, as the Company can generate substantial product revenue, the Company expects to finance its cash needs through a combination of equity offerings, debt financings, collaborations, strategic alliances, licensing arrangements and other sources of funding. If the Company is unable to raise additional funds through equity, debt financings or licensing arrangements when needed, the Company may be required to delay, limit, reduce or terminate product development or future commercialization efforts or grant rights to develop and market products or product candidates that the Company would otherwise prefer to develop and market itself. Based on its current operating plans, the Company believes its cash, cash equivalents and marketable securities of $106.0 million as of June 30, 2017 will be sufficient to fund its anticipated level of operations and capital expenditures for a period of at least one year from the issuance date of this Quarterly Report. The condensed consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries Zafgen Securities Corporation, Zafgen Australia Pty Limited, and Zafgen Animal Health, LLC. All intercompany balances and transactions have been eliminated. Unaudited Interim Financial Information The condensed consolidated balance sheet as of December 31, 2016 was derived from the Company’s audited financial statements, but does not include all disclosures required by accounting principles generally accepted in the United States of America, or GAAP. The accompanying unaudited condensed consolidated financial statements as of June 30, 2017 and for the three and six months ended June 30, 2017 and 2016, have been prepared by the Company, pursuant to the rules and regulations of the Securities and Exchange Commission, or SEC, for interim financial statements. Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted pursuant to such rules and regulations. However, the Company believes that the disclosures are adequate to make the information presented not misleading. These condensed consolidated financial statements should be read in conjunction with the Company’s audited consolidated financial statements and the notes thereto for the year ended December 31, 2016, included in the Company’s Annual Report on Form 10-K, for the year ended December 31, 2016, on file with the SEC. In the opinion of management, all adjustments, consisting only of normal recurring adjustments necessary for a fair statement of the Company’s condensed consolidated financial position as of June 30, 2017 and condensed consolidated results of operations and cash flows for the three and six months ended June 30, 2017 and 2016 have been made. The results of operations for the three and six months ended June 30, 2017 are not necessarily indicative of the results of operations that may be expected for the year ending December 31, 2017.

Summary of Significant Accounting Policies

6 Months Ended

Jun. 30, 2017

Accounting Policies [Abstract]

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Use of Estimates

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities as of the date of the condensed consolidated financial statements, and the reported amounts of expenses during the reporting periods. Significant estimates and assumptions reflected in these condensed consolidated financial statements include, but are not limited to, the accrual of research and development expenses and the valuation of stock-based awards. Estimates are periodically reviewed in light of changes in circumstances, facts and experience. Actual results could differ from the Company’s estimates.

Marketable securities

Marketable securities consist of investments with original maturities greater than ninety days. The Company has classified its investments with maturities beyond one year as short term, based on their highly liquid nature and because such marketable securities represent the investment of cash that is available for current operations. The Company considers its investment portfolio of investments as available-for-sale. Accordingly, these investments are recorded at fair value, which is based on quoted market prices. Unrealized gains and losses are reported as a component of accumulated other comprehensive income (loss) in stockholders’ equity. Realized gains and losses and declines in value judged to be other than temporary are included as a component of other income (expense), net based on the specific identification method. When determining whether a decline in value is other than temporary, the Company considers various factors, including whether the Company has the intent to sell the security, and whether it is more likely than not that the Company will be required to sell the security prior to recovery of its amortized cost basis. Fair value is determined based on quoted market prices.

Net Income (Loss) Per Share

Basic net income (loss) per share is computed by dividing the net income (loss) attributable to common stockholders by the weighted average number of common shares outstanding for the period. Diluted net income (loss) per share attributable to common stockholders is computed by dividing the diluted net income (loss) attributable to common stockholders by the weighted average number of common shares, including potential dilutive common shares assuming the dilutive effect of outstanding stock options and unvested restricted common shares, as determined using the treasury stock method. For periods in which the Company has reported net losses, diluted net loss per common share attributable to common stockholders is the same as basic net loss per common share attributable to common stockholders, since dilutive common shares are not assumed to have been issued if their effect is antidilutive.

The Company excluded the following common stock equivalents, outstanding as of June 30, 2017 and 2016, from the computation of diluted net loss per share for the three months ended June 30, 2017 and 2016 because they had an anti-dilutive impact due to the net loss incurred for the periods:


	As of June 30,
	2017		2016
Options to purchase common stock		4,185,866		3,976,995
Unvested restricted common stock		11,065		9,955

	4,196,931		3,986,950

Recently Issued and Adopted Accounting Pronouncements

In May 2014, the Financial Accounting Standards Board (the “FASB”) issued ASU No. 2014-09, Revenue from Contracts with Customers (Topic 606), which supersedes all existing revenue recognition requirements, including most industry-specific guidance. The new standard requires a company to recognize revenue when it transfers goods or services to customers in an amount that reflects the consideration that the company expects to receive for those goods or services. The FASB has continued to issue accounting standards updates to clarify and provide implementation guidance related to Revenue from Contracts with Customers, including ASU 2016-08, Revenue from Contract with Customers: Principal versus Agent Considerations, ASU 2016-10, Revenue from Contracts with Customers: Identifying Performance Obligations and Licensing, and ASU 2016-12, Revenue from Contracts with Customers: Narrow-Scope Improvements and Practical Expedients. These amendments address a number of areas, including the entity’s identification of its performance obligations in a contract, collectability, non-cash consideration, presentation of sales tax and an entity’s evaluation of the nature of its promise to grant a license of intellectual property and whether or not that revenue is recognized over time or at a point in time. These new standards will be effective for the Company beginning January 1, 2018. The Company early adopted the standard as of January 1, 2017, however there is no impact of this new guidance on its condensed consolidated financial statements as it does not currently have any revenue generating arrangements.

In February 2016, the FASB issued ASU No. 2016-02, Leases. This guidance will require that lease arrangements longer than 12 months result in an entity recognizing an asset and liability equal to the present value of the lease payments in the statement of financial position. This guidance is effective for annual periods beginning after December 15, 2018, and interim periods therein. This standard requires a modified retrospective transition approach for all leases existing at, or entered into after, the date of initial application, with an option to use certain transition relief. Early adoption is permitted. The Company is evaluating the effect that this guidance will have on its condensed consolidated financial statements.

In March 2016, the FASB issued ASU No. 2016-09, Improvements to Employee Share-Based Payment Accounting. This standard was adopted on January 1, 2017 on a modified retrospective basis. As a result the Company has made an accounting policy election to account for forfeitures as they occur. The adoption of this guidance also requires excess tax benefits and tax deficiencies be recorded in the income statement as opposed to additional paid-in capital when the awards vest or are settled. The adoption of this guidance had an immaterial impact on the Company’s condensed consolidated financial statements as of and for the three and six months ended June 30, 2017.

In August 2016, the FASB issued ASU No. 2016-15, Statement of Cash Flows: Classification of Certain Cash Receipts and Cash Payments. This guidance addresses the presentation and classification of certain cash receipts and cash payments in the statement of cash flows. The standard will be effective for annual periods beginning after December 15, 2017, and interim periods therein. Early adoption is permitted. The Company is evaluating the effect that this guidance will have on its condensed consolidated financial statements.

In May 2017, the FASB issued ASU No. 2017-09, Compensation – Stock Compensation: Scope of Modification Accounting. This guidance addresses which changes to the terms or conditions of a share-based payment award require an entity to apply modification accounting. The standard will be effective for annual periods beginning after December 15, 2017, and interim periods therein. Early adoption is permitted. The Company is evaluating the effect that this guidance will have on its condensed consolidated financial statements.

Fair Value Measurements and Marketable Securities

6 Months Ended

Jun. 30, 2017

Fair Value Disclosures [Abstract]

Fair Value Measurements and Marketable Securities

3. Fair Value Measurements and Marketable Securities

Fair Value Measurements

The following tables present information about the Company’s financial assets that have been measured at fair value as of June 30, 2017 and December 31, 2016, and indicate the fair value of the hierarchy of the valuation inputs utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize quoted prices (unadjusted) in active markets for identical assets or liabilities. Fair value determined by Level 2 inputs utilize observable inputs other than Level 1 prices, such as quoted prices, for similar assets or liabilities, quoted market prices in markets that are not active or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the related assets or liabilities. Fair values determined by Level 3 inputs are unobservable data points for the asset or liability, and include situations where there is little, if any, market activity for the asset or liability.

The following tables summarize the Company’s cash equivalents and marketable securities as of June 30, 2017 and December 31, 2016:


	June 30, 2017
	Total		Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
	(in thousands)
Cash equivalents:
Money market funds	$	25,771	$	25,771	$	—	$	—
Commercial paper		1,997		—		1,997		—

Total cash equivalents		27,768		25,771		1,997		—

Marketable securities:
Corporate bonds		55,077		—		55,077		—
Commercial paper		19,189		—		19,189		—

Total marketable securities		74,266		—		74,266		—

Total cash equivalents and marketable securities	$	102,034	$	25,771	$	76,263	$	—


	December 31, 2016
	Total		Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
	(in thousands)
Cash equivalents:
Money market funds	$	22,091	$	22,091	$	—	$	—
Commercial paper		2,997		—		2,997		—
Corporate bonds		1,500		—		1,500		—

Total cash equivalents		26,588		22,091		4,497		—

Marketable securities:
Corporate bonds		69,622		—		69,622		—
Commercial paper		27,220		—		27,220		—

Total marketable securities		96,842		—		96,842		—

Total cash equivalents and marketable securities	$	123,430	$	22,091	$	101,339	$	—

The carrying amounts reflected in the condensed consolidated balance sheets for tax incentive receivable, accounts payable, and accrued expenses approximate fair value due to their short-term maturities. The carrying value of the Company’s outstanding notes payable approximates fair value (a Level 2 fair value measurement), reflecting interest rates currently available to the Company.

Marketable Securities

The following tables summarize the Company’s marketable securities as of June 30, 2017 and December 31, 2016:


	June 30, 2017
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
Assets:
Corporate bonds (due within 1 year)	$	55,112	$	—	$	(35	)	$	55,077
Commercial paper (due within 1 year)		19,193		—		(4	)		19,189

	$	74,305	$	—	$	(39	)	$	74,266


	December 31, 2016
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
Assets:
Corporate bonds (due within 1 year)	$	68,777	$	—	$	(54	)	$	68,723
Corporate bonds (due after 1 year through 2 years)		901		—		(2	)		899
Commercial paper (due within 1 year)		27,244		—		(24	)		27,220

	$	96,922	$	—	$	(80	)	$	96,842

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Accrued Expenses

6 Months Ended

Jun. 30, 2017

Payables and Accruals [Abstract]

Accrued Expenses

4. Accrued Expenses

Accrued expenses consisted of the following as of June 30, 2017 and December 31, 2016:


	June 30, 2017		December 31, 2016
	(in thousands)
Accrued payroll and related expenses	$	1,241	$	2,008
Accrued research and development expenses		1,073		892
Accrued professional fees		293		347
Accrued restructuring		—		376
Accrued other		102		110

	$	2,709	$	3,733

Notes Payable	6 Months Ended
Notes Payable	Jun. 30, 2017
Debt Disclosure [Abstract]
Notes Payable	5. Notes Payable The Company has outstanding amounts due under a loan and security agreement with Oxford Finance LLC and Midcap Financial, or the 2014 Credit Facility, entered into in March 2014. All promissory notes issued under the 2014 Credit Facility are collateralized by substantially all of the Company’s personal property, other than its intellectual property. There are no financial covenants associated with the 2014 Credit Facility; however, there are negative covenants restricting the Company’s activities, including limitations on dispositions, mergers or acquisitions; encumbering or granting a security interest in its intellectual property; incurring indebtedness or liens; paying dividends; making certain investments; and certain other business transactions. During the three months ended June 30, 2017 and 2016, the Company recognized less than $0.1 million and $0.1 million, respectively, of interest expense related to the 2014 Credit Facility. During the six months ended June 30, 2017 and 2016, the Company recognized $0.1 million and $0.3 million, respectively, of interest expense related to the 2014 Credit Facility. The effective annual interest rate of the outstanding debt under the 2014 Credit Facility is approximately 10.8%.

Stock-Based Awards

6 Months Ended

Jun. 30, 2017

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Stock-Based Awards

6. Stock-Based Awards

The Company grants equity awards under its 2014 Stock Option and Incentive Plan, or the 2014 Stock Option Plan, and is authorized to issue common stock under its 2014 Employee Stock Purchase Plan. The Company also has outstanding stock-based awards under its Amended and Restated 2006 Stock Option Plan but is no longer granting awards under this plan. As of June 30, 2017, 2,014,395 shares are available for grant under the 2014 Stock Option Plan, including 1,093,302 shares automatically added to the 2014 Stock Option Plan on January 1, 2017 as a result of a provision in the 2014 Stock Option Plan.

The Company recorded stock-based compensation expense related to stock options and restricted common stock in the following expense categories within its condensed consolidated statements of operations:


	Three Months Ended June 30,				Six Months Ended June 30,
	2017		2016		2017		2016
	(in thousands)
Research and development	$	877	$	1,002	$	1,733	$	1,830
General and administrative	$	1,225		1,852		2,370		3,780

	$	2,102	$	2,854	$	4,103	$	5,610

Commitments and Contingencies

6 Months Ended

Jun. 30, 2017

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

7. Commitments and Contingencies

Leases

The Company has a lease for office space in Boston, Massachusetts, effective as of July 28, 2014, with a term expiring July 31, 2017 and an option to extend the lease for three additional years. In March 2015, the Company entered into an operating lease for additional office space in Boston, Massachusetts, effective as of April 15, 2015, with a term expiring on July 31, 2017, and two options to extend this lease for three additional years each. In October 2015, the Company entered into an operating lease for office space in San Diego, California, effective as of October 1, 2015, with a term expiring on September 30, 2019, and an option to extend this lease for five additional years. In January 2017, the Company extended the leases for both office spaces in Boston, Massachusetts with new terms expiring on July 31, 2020. As of July 31, 2017, the Company negotiated the financial terms of these extensions with additional minimum lease payments of $0.2 million for the remainder of 2017, $0.4 million for the years 2018 and 2019 and $0.2 million for 2020 not reflected in the table below. The Company also has the option to extend both of these leases in Boston, Massachusetts for an additional three years. With the landlord’s consent, the Company has subleased 2,976 square feet of office space in Boston, Massachusetts to an unrelated third party which began on January 1, 2017 and expires on June 30, 2018. The Company expects to receive approximately $0.2 million in sublease rental income during the sublease period.

Future minimum lease payments for its operating leases as of June 30, 2017 were as follows:


Year Ending December 31,
(in thousands)
2017 (July to December)	$	80
2018		106
2019		82

	$	268

During the three months ended June 30, 2017 and 2016, the Company recognized $0.1 million of rental expense related to office space. During the six months ended June 30, 2017 and 2016, the Company recognized $0.2 million of rental expense related to office space.

Intellectual Property Licenses

The Company has acquired exclusive rights to develop patented compounds and related know-how for beloranib under two licensing agreements with two third parties in the course of its research and development activities. The licensing rights obligate the Company to make payments to the licensors for license fees, milestones, license maintenance fees and royalties. The Company is also responsible for patent prosecution costs.

As of June 30, 2017, the Company is obligated to make additional milestone payments of up to $12.3 million upon reaching certain pre-commercialization milestones, such as clinical trials and government approvals (including the U.S. Food and Drug Administration, or FDA, approval of a New Drug Application, or NDA), and up to $12.5 million upon reaching certain product commercialization milestones related to the development of beloranib. Under one of the license agreements, the Company is also obligated to pay up to $1.3 million with respect to each subsequent licensed product, if any, that is a new chemical entity. In addition, the Company will owe single-digit royalties on sales of commercial products developed using these licensed technologies, if any.

There were no milestones achieved during the three or six months ended June 30, 2017 or 2016. The Company is also obligated to pay to the licensors a percentage of fees received if and when the Company sublicenses the technology. As of June 30, 2017, the Company has not yet developed a commercial product using the licensed technologies and it has not entered into any sublicense agreements for the technologies.

Indemnification Agreements

In the ordinary course of business, the Company may provide indemnification of varying scope and terms to vendors, lessors, business partners, and other parties with respect to certain matters including, but not limited to, losses arising out of breach of such agreements or from intellectual property infringement claims made by third parties. In addition, the Company has entered into indemnification agreements with members of management team and the board of directors of the Company that will require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors or officers. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is, in many cases, unlimited. To date, the Company has not incurred any material costs as a result of such indemnifications. The Company does not believe that the outcome of any claims under indemnification arrangements will have a material effect on its financial position, results of operations or cash flows, and it has not accrued any liabilities related to such obligations in its condensed consolidated financial statements as of June 30, 2017.

Legal Proceedings

The Company accrues a liability for legal contingencies when it believes that it is both probable that a liability has been incurred and that the Company can reasonably estimate the amount of the loss. The Company reviews these accruals and adjusts them to reflect ongoing negotiations, settlements, rulings, advice of legal counsel and other relevant information. To the extent new information is obtained and the views on the probable outcomes of claims, suits, assessments, investigations or legal proceedings change, changes in the Company’s accrued liabilities would be recorded in the period in which such determination is made. In addition, in accordance with the relevant authoritative guidance, for any matters in which the likelihood of material loss is at least reasonably possible, the Company will provide disclosure of the possible loss or range of loss. If a reasonable estimate cannot be made, however, the Company will provide disclosure to that effect. The Company expenses legal costs as they are incurred.

On October 21, 2015, a purported stockholder of the Company filed a putative class action lawsuit in the U.S. District Court for the District of Massachusetts, against the Company and Thomas E. Hughes, captioned Aviad Bessler v. Zafgen, Inc. and Thomas E. Hughes, No. 1:15-cv-13618. An amended complaint was filed on February 22, 2016. The amended complaint alleges violations of Sections 10(b) and 20(a) of the Securities Exchange Act of 1934 and SEC Rule 10b-5 based on allegedly false and misleading statements and omissions regarding the Company’s clinical trials for its drug beloranib. On August 9, 2016, the District Court granted the motion to dismiss and dismissed the amended complaint with prejudice. On August 12, 2016, plaintiffs filed a notice of appeal to the First Circuit Court of Appeals and on April 7, 2017, the dismissal with prejudice was affirmed.

The Company may periodically become subject to other legal proceedings and claims arising in connection with ongoing business activities, including claims or disputes related to patents that have been issued or that are pending in the field of research on which the Company is focused. The Company is not aware of any material claims as of June 30, 2017.

Retirement Plan	6 Months Ended
Retirement Plan	Jun. 30, 2017
Retirement Benefits [Abstract]
Retirement Plan	8. Retirement Plan The Company has a Savings Incentive Match Plan, or SIMPLE IRA, for employees. Under the terms of the plan, the Company contributes 2% of an employee’s annual base salary, up to a maximum of the annual Internal Revenue Service compensation limits, for all full-time employees. During the three months ended June 30, 2017 and 2016, the Company recognized less than $0.1 million of expense related to its contributions to the plan. During the six months ended June 30, 2017 and 2016, the Company recognized $0.1 million of expense related to its contributions to the plan.

Australia Research and Development Tax Incentive	6 Months Ended
Australia Research and Development Tax Incentive	Jun. 30, 2017
Research and Development [Abstract]
Australia Research and Development Tax Incentive	9. Australia Research and Development Tax Incentive The Company’s wholly owned subsidiary, Zafgen Australia Pty Limited, which conducts core research and development activities on behalf of the Company, is eligible to receive a 45% refundable tax incentive for qualified research and development activities through December 31, 2016 and 43.5% beginning January 1, 2017. For the three months ended June 30, 2017 and 2016, $0.2 million was recorded as a reduction to research and development expenses in the condensed consolidated statements of operations. For the six months ended June 30, 2017 and 2016, $0.2 million and $0.3 million, respectively, were recorded as a reduction to research and development expenses in the condensed consolidated statements of operations. The refund is denominated in Australian dollars and, therefore, the related receivable is re-measured into U.S. dollars as of each reporting date. For the three months ended June 30, 2017 and 2016, the Company recorded in its condensed consolidated statements of operations unrealized foreign currency exchange gains of nil and losses of less than $0.1 million, respectively, related to this tax incentive receivable. For the six months ended June 30, 2017 and 2016, the Company recorded in its condensed consolidated statements of operations unrealized foreign currency exchange gains of less than $0.1 million related to this tax incentive receivable. As of June 30, 2017 and December 31, 2016, the Company’s tax incentive receivable from the Australian government was $0.6 million and $0.3 million, respectively.

Restructuring

6 Months Ended

Jun. 30, 2017

Restructuring and Related Activities [Abstract]

Restructuring

10. Restructuring

On July 19, 2016, the Company announced that following a comprehensive review of its assets and clinical programs, as well as feedback from regulatory authorities, the Company refocused its resources on development of a differentiated MetAP2 inhibitor, ZGN-1061. As part of the strategic restructuring, the Company reorganized its operations to align with its new priorities focused on ZGN-1061 development. The Company’s workforce was reduced by approximately 31% as of December 2016. The following table summarizes the restructuring reserve for the periods indicated:


	Six Months Ended June 30, 2017			Year Ended December 31, 2016
	(in thousands)
Restructuring reserve beginning balance	$	376		$	—
Restructuring expenses incurred during the period		24			1,223
Amounts paid during the period		(400	)		(847	)

Restructuring reserve ending balance	$	—		$	376

Summary of Significant Accounting Policies (Policies)

6 Months Ended

Jun. 30, 2017

Accounting Policies [Abstract]

Use of Estimates

Use of Estimates

Marketable securities

Marketable securities

Net Income (Loss) Per Share

Net Income (Loss) Per Share


	As of June 30,
	2017		2016
Options to purchase common stock		4,185,866		3,976,995
Unvested restricted common stock		11,065		9,955

	4,196,931		3,986,950

Recently Issued and Adopted Accounting Pronouncements

Recently Issued and Adopted Accounting Pronouncements

- Definition

Disclosure of accounting policy for investments in debt and equity securities that have readily determinable fair values (marketable securities). At a minimum, the disclosure might address accounting policies for investments classified as trading, available for sale, or held to maturity and may include how the entity determines whether impairments of available for sale or held to maturity investments are other than temporary, how the fair values of the entity's securities are determined, and the entity's accounting treatment for transfers between investment categories.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 210
-Section S99
-Paragraph 1
-Subparagraph (SX 210.9-03(6))
-URI http://asc.fasb.org/extlink&oid=6876686&loc=d3e534808-122878

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 944
-SubTopic 210
-Section S99
-Paragraph 1
-Subparagraph (SX 210.7-03(a)(1))
-URI http://asc.fasb.org/extlink&oid=6879938&loc=d3e572229-122910

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SAB Topic 5.M)
-URI http://asc.fasb.org/extlink&oid=65877573&loc=d3e87990-122713

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02(12))
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=84158767&loc=d3e18780-107790

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section S50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6381980&loc=d3e87707-122711

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 320
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=75019621&loc=d3e62652-112803

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02(2))
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 210
-Section S99
-Paragraph 1
-Subparagraph (SX 210.9-03(5))
-URI http://asc.fasb.org/extlink&oid=6876686&loc=d3e534808-122878

+ Details

Summary of Significant Accounting Policies (Tables)

6 Months Ended

Jun. 30, 2017

Accounting Policies [Abstract]

Summary of Common Stock Equivalents Outstanding


	As of June 30,
	2017		2016
Options to purchase common stock		4,185,866		3,976,995
Unvested restricted common stock		11,065		9,955

	4,196,931		3,986,950

Fair Value Measurements and Marketable Securities (Tables)

6 Months Ended

Jun. 30, 2017

Fair Value Disclosures [Abstract]

Summary of Cash Equivalents and Marketable Securities

The following tables summarize the Company’s cash equivalents and marketable securities as of June 30, 2017 and December 31, 2016:


	June 30, 2017
	Total		Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
	(in thousands)
Cash equivalents:
Money market funds	$	25,771	$	25,771	$	—	$	—
Commercial paper		1,997		—		1,997		—

Total cash equivalents		27,768		25,771		1,997		—

Marketable securities:
Corporate bonds		55,077		—		55,077		—
Commercial paper		19,189		—		19,189		—

Total marketable securities		74,266		—		74,266		—

Total cash equivalents and marketable securities	$	102,034	$	25,771	$	76,263	$	—


	December 31, 2016
	Total		Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
	(in thousands)
Cash equivalents:
Money market funds	$	22,091	$	22,091	$	—	$	—
Commercial paper		2,997		—		2,997		—
Corporate bonds		1,500		—		1,500		—

Total cash equivalents		26,588		22,091		4,497		—

Marketable securities:
Corporate bonds		69,622		—		69,622		—
Commercial paper		27,220		—		27,220		—

Total marketable securities		96,842		—		96,842		—

Total cash equivalents and marketable securities	$	123,430	$	22,091	$	101,339	$	—

Summary of Marketable Securities

The following tables summarize the Company’s marketable securities as of June 30, 2017 and December 31, 2016:


	June 30, 2017
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
Assets:
Corporate bonds (due within 1 year)	$	55,112	$	—	$	(35	)	$	55,077
Commercial paper (due within 1 year)		19,193		—		(4	)		19,189

	$	74,305	$	—	$	(39	)	$	74,266


	December 31, 2016
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
Assets:
Corporate bonds (due within 1 year)	$	68,777	$	—	$	(54	)	$	68,723
Corporate bonds (due after 1 year through 2 years)		901		—		(2	)		899
Commercial paper (due within 1 year)		27,244		—		(24	)		27,220

	$	96,922	$	—	$	(80	)	$	96,842

- Definition

Tabular disclosure of available-for-sale securities which includes, but is not limited to, changes in the cost basis and fair value, fair value and gross unrealized gain (loss), fair values by type of security, contractual maturity and classification, amortized cost basis, contracts to acquire securities to be accounted for as available-for-sale, debt maturities, transfers to trading, change in net unrealized holding gain (loss) net of tax, continuous unrealized loss position fair value, aggregate losses qualitative disclosures, other than temporary impairment (OTTI) losses or other disclosures related to available for sale securities.

+ References + Details

Accrued Expenses (Tables)

6 Months Ended

Jun. 30, 2017

Payables and Accruals [Abstract]

Schedule of Accrued Expenses

Accrued expenses consisted of the following as of June 30, 2017 and December 31, 2016:


	June 30, 2017		December 31, 2016
	(in thousands)
Accrued payroll and related expenses	$	1,241	$	2,008
Accrued research and development expenses		1,073		892
Accrued professional fees		293		347
Accrued restructuring		—		376
Accrued other		102		110

	$	2,709	$	3,733

Stock-Based Awards (Tables)

6 Months Ended

Jun. 30, 2017

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Summary of Stock-Based Compensation Expense Related to Stock Options and Restricted Common Stock


	Three Months Ended June 30,				Six Months Ended June 30,
	2017		2016		2017		2016
	(in thousands)
Research and development	$	877	$	1,002	$	1,733	$	1,830
General and administrative	$	1,225		1,852		2,370		3,780

	$	2,102	$	2,854	$	4,103	$	5,610

Commitments and Contingencies (Tables)

6 Months Ended

Jun. 30, 2017

Commitments and Contingencies Disclosure [Abstract]

Schedule of Future Minimum Lease Payments for Operating Leases

Future minimum lease payments for its operating leases as of June 30, 2017 were as follows:


Year Ending December 31,
(in thousands)
2017 (July to December)	$	80
2018		106
2019		82

	$	268

Restructuring (Tables)

6 Months Ended

Jun. 30, 2017

Restructuring and Related Activities [Abstract]

Summary of Restructuring Reserve

The following table summarizes the restructuring reserve for the periods indicated:


	Six Months Ended June 30, 2017			Year Ended December 31, 2016
	(in thousands)
Restructuring reserve beginning balance	$	376		$	—
Restructuring expenses incurred during the period		24			1,223
Amounts paid during the period		(400	)		(847	)

Restructuring reserve ending balance	$	—		$	376

Nature of the Business and Basis of Presentation - Additional Information (Detail) - USD ($) $ in Thousands	6 Months Ended	139 Months Ended
	Jun. 30, 2017	Jun. 30, 2017	Dec. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Entity incorporation date	Nov. 22, 2005
Accumulated deficit	$ (263,907)	$ (263,907)	$ (237,549)
Net proceeds from sale of securities		333,300
Total cash, cash equivalents and marketable securities	$ 106,000	$ 106,000

Summary of Significant Accounting Policies - Summary of Common Stock Equivalents Outstanding (Detail) - shares	6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	4,196,931	3,986,950
Options to Purchase Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	4,185,866	3,976,995
Unvested Restricted Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	11,065	9,955

Fair Value Measurements and Marketable Securities - Summary of Cash Equivalents and Marketable Securities (Detail) - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	$ 27,768	$ 26,588
Marketable securities	74,266	96,842
Total cash equivalents and marketable securities	102,034	123,430
Money Market Funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	25,771	22,091
Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	1,997
Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		1,500
Marketable securities	55,077	69,622
Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		2,997
Marketable securities	19,189	27,220
Quoted Prices in Active Markets, (Level 1) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	25,771	22,091
Total cash equivalents and marketable securities	25,771	22,091
Quoted Prices in Active Markets, (Level 1) [Member] \| Money Market Funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	25,771	22,091
Significant Other Observable Inputs (Level 2) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	1,997	4,497
Marketable securities	74,266	96,842
Total cash equivalents and marketable securities	76,263	101,339
Significant Other Observable Inputs (Level 2) [Member] \| Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	1,997
Significant Other Observable Inputs (Level 2) [Member] \| Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		1,500
Marketable securities	55,077	69,622
Significant Other Observable Inputs (Level 2) [Member] \| Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		2,997
Marketable securities	$ 19,189	$ 27,220

Fair Value Measurements and Marketable Securities - Summary of Marketable Securities (Detail) - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 74,305	$ 96,922
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(39)	(80)
Fair Value	74,266	96,842
Corporate Bonds (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	55,112	68,777
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(35)	(54)
Fair Value	55,077	68,723
Commercial Paper (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	19,193	27,244
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(4)	(24)
Fair Value	$ 19,189	27,220
Corporate Bonds (Due After 1 Year Through 2 Years) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost		901
Gross Unrealized Gains		0
Gross Unrealized Losses		(2)
Fair Value		$ 899

Accrued Expenses - Schedule of Accrued Expenses (Detail) - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Payables and Accruals [Abstract]
Accrued payroll and related expenses	$ 1,241	$ 2,008
Accrued research and development expenses	1,073	892
Accrued professional fees	293	347
Accrued restructuring		376
Accrued other	102	110
Accrued expenses	$ 2,709	$ 3,733

Notes Payable - Additional Information (Detail) - 2014 Credit Facility [Member] - USD ($)	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Debt Instrument [Line Items]
Covenants under credit facility			There are no financial covenants associated with the 2014 Credit Facility; however, there are negative covenants restricting the Company’s activities, including limitations on dispositions, mergers or acquisitions; encumbering or granting a security interest in its intellectual property; incurring indebtedness or liens; paying dividends; making certain investments; and certain other business transactions.
Secured Debt [Member]
Debt Instrument [Line Items]
Interest expense on credit facility		$ 100,000	$ 100,000	$ 300,000
Effective annual interest rate	10.80%		10.80%
Maximum [Member] \| Secured Debt [Member]
Debt Instrument [Line Items]
Interest expense on credit facility	$ 100,000

Stock-Based Awards - Additional Information (Detail) - 2014 Stock Option and Incentive Plan [Member] - shares	Jan. 01, 2017	Jun. 30, 2017
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares added to plan	1,093,302
Shares available for grant		2,014,395

Stock-Based Awards - Summary of Stock-Based Compensation Expense Related to Stock Options and Restricted Common Stock (Detail) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 2,102	$ 2,854	$ 4,103	$ 5,610
Research and Development [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	877	1,002	1,733	1,830
General and Administrative [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 1,225	$ 1,852	$ 2,370	$ 3,780

Commitments and Contingencies - Additional Information (Detail)					1 Months Ended	3 Months Ended		6 Months Ended		18 Months Ended
	Jan. 01, 2017 ft²	Oct. 01, 2015	Apr. 15, 2015 Option	Jul. 28, 2014	Jan. 31, 2017	Jun. 30, 2017 USD ($)	Jun. 30, 2016 USD ($)	Jun. 30, 2017 USD ($)	Jun. 30, 2016 USD ($)	Jun. 30, 2018 USD ($)
Other Commitments [Line Items]
2017 (July to December)						$ 80,000		$ 80,000
2018						106,000		106,000
2019						82,000		82,000
Operating lease, rental expense						100,000	$ 100,000	200,000	$ 200,000
Subsequent Licensed Product [Member]
Other Commitments [Line Items]
Licensing fees per product maximum						1,300,000		1,300,000
Development Based Milestones [Member]
Other Commitments [Line Items]
Milestone payments due						0	$ 0	$ 0	$ 0
Boston Office Space [Member]
Other Commitments [Line Items]
Lease expiration date				Jul. 31, 2017	Jul. 31, 2020			Jul. 31, 2020
Lease extension period				3 years				3 years
2017 (July to December)						200,000		$ 200,000
2018						400,000		400,000
2019						400,000		400,000
2020						200,000		$ 200,000
Boston Office Space [Member] \| Unrelated Third Party Member
Other Commitments [Line Items]
Subleased area \| ft²	2,976
Sublease expiration date	Jun. 30, 2018
Boston Office Space [Member] \| Unrelated Third Party Member \| Scenario, Forecast [Member]
Other Commitments [Line Items]
Sublease rental income										$ 200,000
Additional Boston Office Space [Member]
Other Commitments [Line Items]
Lease expiration date			Jul. 31, 2017					Jul. 31, 2020
Lease extension period			3 years
Number of options to extend lease \| Option			2
San Diego Office Space [Member]
Other Commitments [Line Items]
Lease expiration date		Sep. 30, 2019
Lease extension period		5 years
Maximum [Member] \| Pre Commercialization Milestones [Member]
Other Commitments [Line Items]
Milestone payments						12,300,000		$ 12,300,000
Maximum [Member] \| Product Commercialization Milestones [Member]
Other Commitments [Line Items]
Milestone payments						$ 12,500,000		$ 12,500,000

Commitments and Contingencies - Schedule of Future Minimum Lease Payments for Operating Leases (Detail) $ in Thousands	Jun. 30, 2017 USD ($)
Commitments and Contingencies Disclosure [Abstract]
2017 (July to December)	$ 80
2018	106
2019	82
Total	$ 268

Retirement Plan - Additional Information (Detail) - USD ($)	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Defined Contribution Plan Disclosure [Line Items]
Percentage of employer's contribution on employee's base salary			2.00%
Contribution expense			$ 100,000	$ 100,000
Maximum [Member]
Defined Contribution Plan Disclosure [Line Items]
Contribution expense	$ 100,000	$ 100,000

Australia Research and Development Tax Incentive - Additional Information (Detail) - USD ($)	3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016	Dec. 31, 2016
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency transaction gains (losses)			$ 21,000	$ 108,000
Zafgen Australia Pty Limited [Member]
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency transaction gains (losses)	$ 0
Zafgen Australia Pty Limited [Member] \| Australia [Member]
Research and Development Tax Incentive [Line Items]
Tax incentive receivable	600,000		$ 600,000		$ 300,000
Zafgen Australia Pty Limited [Member] \| Research and Development [Member]
Research and Development Tax Incentive [Line Items]
Percentage of refundable tax incentive			43.50%		45.00%
Reduction to research and development expenses	$ 200,000	$ 200,000	$ 200,000	300,000
Zafgen Australia Pty Limited [Member] \| Maximum [Member]
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency transaction gains (losses)		$ (100,000)	$ 100,000	$ 100,000

Restructuring - Additional Information (Detail)	1 Months Ended
Restructuring - Additional Information (Detail)	Dec. 31, 2016
Restructuring and Related Activities [Abstract]
Percentage of workforce reduction	31.00%

Restructuring - Summary of Restructuring Reserve (Detail) - USD ($) $ in Thousands	6 Months Ended	12 Months Ended
	Jun. 30, 2017	Dec. 31, 2016
Restructuring Reserve [Abstract]
Restructuring reserve beginning balance	$ 376
Restructuring expenses incurred during the period	24	$ 1,223
Amounts paid during the period	$ (400)	(847)
Restructuring reserve ending balance		$ 376