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Document and Entity Information - shares	3 Months Ended
Document and Entity Information - shares	Mar. 31, 2018	Apr. 30, 2018
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Mar. 31, 2018
Document Fiscal Year Focus	2018
Document Fiscal Period Focus	Q1
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		27,563,346

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Mar. 31, 2018	Dec. 31, 2017
Current assets:
Cash and cash equivalents	$ 45,731	$ 40,777
Marketable securities	43,339	61,275
Tax incentive receivable	932	946
Prepaid expenses and other current assets	1,420	1,927
Total current assets	91,422	104,925
Tax incentive receivable	581
Property and equipment, net	479	528
Other assets	132	57
Total assets	92,614	105,510
Current liabilities:
Accounts payable	3,796	3,020
Accrued expenses	3,661	4,273
Total current liabilities	7,457	7,293
Notes payable, long-term	20,160	20,000
Total liabilities	27,617	27,293
Commitments and contingencies (Note 7)
Stockholders' equity:
Preferred stock; $0.001 par value per share; 5,000,000 shares authorized as of March 31, 2018 and December 31, 2017; no shares issued and outstanding as of March 31, 2018 and December 31, 2017
Common stock, $0.001 par value per share; 115,000,000 shares authorized as of March 31, 2018 and December 31, 2017; 27,558,883 and 27,489,457 shares issued and outstanding as of March 31, 2018 and December 31, 2017, respectively	28	27
Additional paid-in capital	370,551	367,825
Accumulated deficit	(305,533)	(289,577)
Accumulated other comprehensive loss	(49)	(58)
Total stockholders' equity	64,997	78,217
Total liabilities and stockholders' equity	$ 92,614	$ 105,510

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Mar. 31, 2018	Dec. 31, 2017
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	27,558,883	27,489,457
Common stock, shares outstanding	27,558,883	27,489,457

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2018	Mar. 31, 2017
Income Statement [Abstract]
Revenue	$ 0	$ 0
Operating expenses:
Research and development	12,433	9,677
General and administrative	3,269	3,588
Total operating expenses	15,702	13,265
Loss from operations	(15,702)	(13,265)
Other income (expense):
Interest income	267	227
Interest expense	(458)	(73)
Foreign currency transaction gains (losses), net	(63)	100
Total other income (expense), net	(254)	254
Net loss	$ (15,956)	$ (13,011)
Net loss per share, basic and diluted	$ (0.58)	$ (0.48)
Weighted average common shares outstanding, basic and diluted	27,541,594	27,350,673
Comprehensive loss:
Net loss	$ (15,956)	$ (13,011)
Other comprehensive loss:
Unrealized gain on marketable securities	9	17
Total other comprehensive income (loss)	9	17
Total comprehensive loss	$ (15,947)	$ (12,994)

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2018	Mar. 31, 2017
Cash flows from operating activities:
Net loss	$ (15,956)	$ (13,011)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation expense	2,466	2,001
Non-cash interest expense		7
Depreciation expense	50	41
Unrealized foreign currency transaction losses (gains)	14	(21)
Premium on marketable securities	(3)	(210)
Amortization of premium on marketable securities	(11)	64
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	507	(20)
Tax incentive receivable	(581)
Accounts payable	776	(662)
Accrued expenses	(527)	132
Net cash used in operating activities	(13,265)	(11,679)
Cash flows from investing activities:
Proceeds from sales and maturities of marketable securities	30,839	41,493
Purchases of marketable securities	(12,880)	(32,792)
Purchases of property and equipment	(1)	(10)
Net cash provided by investing activities	17,958	8,691
Cash flows from financing activities:
Repayments of notes payable		(772)
Proceeds from exercise of common stock options and employee stock purchase plan	261	40
Net cash provided by (used in) financing activities	261	(732)
Net increase (decrease) in cash and cash equivalents	4,954	(3,720)
Cash and cash equivalents at beginning of period	40,777	32,352
Cash and cash equivalents at end of period	45,731	28,632
Supplemental disclosure of cash flow information:
Cash paid for interest	$ 198	$ 59

Nature of the Business and Basis of Presentation	3 Months Ended
Nature of the Business and Basis of Presentation	Mar. 31, 2018
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 clinical-stage biopharmaceutical company leveraging its proprietary knowledge of the methionine aminopeptidase 2 (“MetAP2”) pathway to develop novel therapies for patients affected by a range of complex metabolic diseases. Zafgen has pioneered the study of MetAP2 inhibitors in both common and rare metabolic disorders, and its current disease areas of focus are type 2 diabetes, Prader-Willi syndrome (“PWS”) and liver diseases. The Company’s lead product candidate is ZGN-1061, a MetAP2 inhibitor with unique properties that maximize impact on metabolic parameters relevant to the treatment of type 2 diabetes and other related metabolic disorders, is in Phase 2 clinical development. In January 2018, the Company announced advancement of its highly optimized MetAP2 development candidate ZGN-1258, and in the first quarter of 2018, initiated investigational new drug (“IND”) application enabling nonclinical efforts for evaluation of ZGN-1258 in the treatment of people affected by PWS. 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 nonclinical 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 March 31, 2018, the Company had an accumulated deficit of $305.5 million. From its inception through March 31, 2018, 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. As disclosed in Note 5 to the condensed consolidated financial statements, the Company has a term loan with an aggregate principal balance of $20.0 million as of March 31, 2018. The loan agreement requires that the Company maintain certain minimum liquidity at all times, which as of March 31, 2018, was approximately $21.0 million. If the minimum liquidity covenant is not met, the Company may be required to repay the loans prior to scheduled maturity dates. 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. Based on its current operating plans, the Company believes its cash, cash equivalents and marketable securities of $89.1 million as of March 31, 2018 will be sufficient to fund its anticipated level of operations, capital expenditures and satisfy debt repayments for a period of at least one year from the issuance date of this Quarterly Report. If the Company is unable to raise additional funds through equity or debt financings, 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. 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, 2017 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 March 31, 2018 and for the three months ended March 31, 2018 and 2017, 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, 2017, included in the Company’s Annual Report on Form 10-K, for the year ended December 31, 2017, 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 March 31, 2018 and condensed consolidated results of operations and cash flows for the three months ended March 31, 2018 and 2017 have been made. The results of operations for the three months ended March 31, 2018 are not necessarily indicative of the results of operations that may be expected for the year ending December 31, 2018.

Summary of Significant Accounting Policies

3 Months Ended

Mar. 31, 2018

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 March 31, 2018 and 2017, from the computation of diluted net loss per share for the three months ended March 31, 2018 and 2017 because they had an anti-dilutive impact due to the net loss incurred for the periods:


	As of March 31,
	2018		2017
Options to purchase common stock		5,839,261		4,048,377
Unvested restricted common stock		13,393		16,597

		5,852,654		4,064,974

Recently Issued and Adopted Accounting Pronouncements

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 consolidated financial statements.

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. This standard will be effective for annual periods beginning after December 15, 2017, and interim periods therein. The adoption of this guidance had no impact on the Company’s condensed consolidated financial statements as of and for the three months ended March 31, 2018.

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. This standard will be effective for annual periods beginning after December 15, 2017, and interim periods therein. The adoption of this guidance had no impact on the Company’s condensed consolidated financial statements as of and for the three months ended March 31, 2018.

Fair Value Measurements and Marketable Securities

3 Months Ended

Mar. 31, 2018

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 March 31, 2018 and December 31, 2017 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. During the three months ended March 31, 2018 and the year ended December 31, 2017, there were no transfers between Level 1 and Level 2 financial assets.

The following tables summarize the Company’s cash equivalents and marketable securities as of March 31, 2018 and December 31, 2017:


	March 31, 2018
	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	$	28,311	$	28,311	$	—	$	—
Commercial paper		6,089		—		6,089		—
Corporate bonds		1,198		—		1,198		—

Total cash equivalents		35,598		28,311		7,287		—

Marketable securities:
Corporate bonds		27,214		—		27,214		—
Commercial paper		16,125		—		16,125		—

Total marketable securities		43,339		—		43,339		—

Total cash equivalents and marketable securities	$	78,937	$	28,311	$	50,626	$	—


	December 31, 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	$	15,802	$	15,802	$	—	$	—
Commercial paper		998		—		998		—
Corporate bonds		549		—		549		—

Total cash equivalents		17,349		15,802		1,547		—

Marketable securities:
Corporate bonds		50,844		—		50,844		—
Commercial paper		9,951		—		9,951		—
Certificates of deposit		480		—		480		—

Total marketable securities		61,275		—		61,275		—

Total cash equivalents and marketable securities	$	78,624	$	15,802	$	62,822	$	—

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 March 31, 2018 and December 31, 2017:


	March 31, 2018
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
Assets:
Corporate bonds (due within 1 year)	$	27,250	$	—	$	(36	)	$	27,214
Commercial paper (due within 1 year)		16,136		—		(11	)		16,125

	$	43,386	$	—	$	(47	)	$	43,339


	December 31, 2017
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
Assets:
Corporate bonds (due within 1 year)	$	50,892	$	—	$	(48	)	$	50,844
Commercial paper (due within 1 year)		9,961		—		(10	)		9,951
Certificates of deposit (due within 1 year)		480		—		—			480

	$	61,333	$	—	$	(58	)	$	61,275

- 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

3 Months Ended

Mar. 31, 2018

Payables and Accruals [Abstract]

Accrued Expenses

4. Accrued Expenses

Accrued expenses consisted of the following as of March 31, 2018 and December 31, 2017:


	March 31, 2018		December 31, 2017
	(in thousands)
Accrued research and development expenses	$	2,075	$	1,647
Accrued payroll and related expenses		836		2,229
Accrued professional fees		564		292
Accrued other		186		105

	$	3,661	$	4,273

Notes Payable

3 Months Ended

Mar. 31, 2018

Debt Disclosure [Abstract]

Notes Payable

5. Notes Payable

On December 29, 2017, the Company entered into a loan and security agreement with Silicon Valley Bank (the “Term Loan”). The Term Loan provided for borrowings of $20.0 million. On December 29, 2017, the Company received proceeds of $20.0 million from the issuance of a promissory note. The promissory note issued under the Term Loan is collateralized by substantially all of the Company’s personal property, other than its intellectual property.

Upon entering into this Term Loan, the Company is obligated to make monthly, interest-only payments until March 29, 2019 and, thereafter, to pay 33 consecutive, equal monthly installments of principal and interest from April 1, 2019 through December 1, 2021. The outstanding Term Loan bears a variable interest at an annual rate of 1.25% above the prime rate, which at March 31, 2018 was 4.75%. In addition, a final payment equal to 8.0% of the Term Loan is due upon the earlier of the maturity date, acceleration of the Term Loan or prepayment of all or part of the Term Loan. The Company accrues the final payment amount of $1.6 million, to outstanding debt by charges to interest expense using the effective-interest method from the date of issuance through the maturity date.

Additionally, the Company, as the borrower, is required to maintain a minimum cash, cash equivalents and marketable securities balance at Silicon Valley Bank of no less than 105% of the total outstanding principal balance of the Term Loan, which as of March 31, 2018 and December 31, 2017 was $21.0 million.

Further, as of 45 days after the Term Loan was entered in, the Company met its obligation to maintain a balance of unrestricted cash, cash equivalents and marketable securities at Silicon Valley Bank in an amount not less than the greater of (i) $55.0 million and (ii) sixty-five percent (65%) of all the Company’s cash, cash equivalents and marketable securities. If the Company does not meet this requirement it will not be considered an event of default provided it immediately secures 87.5% of the principal balance in a restricted cash account.

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; permit the aggregate value of cash maintained by its Australian subsidiary not to exceed $4.0 million and certain other business transactions.

The Term Loan also includes events of default, the occurrence and continuation of any of which provides the lenders the right to exercise remedies against the Company and the collateral securing the amounts due under the Term Loan, including cash in the amount of the outstanding balance. These events of default include, among other things, failure to pay any amounts due under the Term Loan, insolvency, the occurrence of a material adverse event, the occurrence of any default under certain other indebtedness and a final judgment against the Company in an amount greater than $0.3 million.

As of March 31, 2018 and December 31, 2017, notes payable was $20.2 million and $20.0 million, respectively.

As of March 31, 2018, the estimated future principal payments due are as follows:


Year Ending December 31,
(in thousands)
2018	$	—
2019		5,454
2020		7,273
2021		7,273

Total	$	20,000

During the three months ended March 31, 2018, the Company recognized $0.5 million of interest expense related to the Term Loan. The effective annual interest rate of the outstanding debt under the Term Loan is approximately 9.2%.

During the three months ended March 31, 2017, the Company recognized $0.1 million of interest expense related to amounts due under its 2014 Credit Facility, which was repaid in full in December 2017. The effective annual interest rate of the debt under the 2014 Credit Facility was approximately 10.8%.

Stock-Based Awards

3 Months Ended

Mar. 31, 2018

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

Stock-Based Awards

6. Stock-Based Awards

The Company’s 2014 Stock Option and Incentive Plan, as amended (the “2014 Plan”) provides for the grant of stock options, stock appreciation rights, restricted stock awards, restricted stock units, unrestricted stock awards, performance-share awards, cash-based awards and dividend equivalent rights to employees, members of the board of directors and consultants of the Company. 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 March 31, 2018, 1,677,858 shares are available for grant under the 2014 Plan, including 1,099,578 shares automatically added to the 2014 Stock Option Plan on January 1, 2018.

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 for the three months ended March 31, 2018 and 2017 as follows:


	Three Months Ended March 31,
	2018		2017
	(in thousands)
Research and development	$	1,572	$	856
General and administrative		894		1,145

	$	2,466	$	2,001

Commitments and Contingencies

3 Months Ended

Mar. 31, 2018

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 January 2017, the Company extended the leases for both office spaces in Boston, Massachusetts with new terms expiring on July 31, 2020. In addition, with the landlord’s consent, the Company has subleased 2,976 square feet of office space in Boston, Massachusetts to an unrelated third party beginning on January 1, 2017 and expiring on December 31, 2018, and the Company expects to receive approximately $0.2 million in sublease rental income. 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.

Future minimum lease payments for its operating leases as of March 31, 2018 were as follows:


Year Ending December 31,
(in thousands)
2018 (April - December)	$	360
2019		464
2020		226
2021		—

	$	1,050

During the three months ended March 31, 2018 and 2017, the Company recognized $0.1 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 March 31, 2018, 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 months ended March 31, 2018 and 2017. 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 March 31, 2018, 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 its management team and its board of directors 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 March 31, 2018.

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.

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 March 31, 2018.

Retirement Plan	3 Months Ended
Retirement Plan	Mar. 31, 2018
Retirement Benefits [Abstract]
Retirement Plan	8. Retirement Plan Effective January 1, 2018, the Company adopted a 401(k) plan for its employees. Under the terms of the plan, the Company contributes 3% of an employee’s annual base salary, up to a maximum of the annual Internal Revenue Service compensation limits, for all full-time employees. The Company terminated its Savings Incentive Match Plan, or SIMPLE IRA as of December 31, 2017. During the three months ended March 31, 2018, the Company recognized $0.1 million of expense related to its contributions to the 401(k) plan. During the three months ended March 31, 2017, the Company recognized less than $0.1 million of expense related to its contributions to the SIMPLE IRA plan.

Australia Research and Development Tax Incentive	3 Months Ended
Australia Research and Development Tax Incentive	Mar. 31, 2018
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 43.5% refundable tax incentive for qualified research and development activities. For the three months ended March 31, 2018 and 2017, $0.6 million and nil, respectively, were recorded as a reduction to research and development expenses in the condensed consolidated statements of operations. These amounts represented 43.5% of the Company’s qualified research and development spending in Australia. 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 March 31, 2018 and 2017, the Company recorded in its condensed consolidated statements of operations unrealized foreign currency exchange gains (losses) of less than $0.1 million related to this tax incentive receivable. As of March 31, 2018 and December 31, 2017, the Company’s tax incentive receivable from the Australian government was $1.5 million and $0.9 million, respectively.

Summary of Significant Accounting Policies (Policies)

3 Months Ended

Mar. 31, 2018

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 March 31,
	2018		2017
Options to purchase common stock		5,839,261		4,048,377
Unvested restricted common stock		13,393		16,597

		5,852,654		4,064,974

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)

3 Months Ended

Mar. 31, 2018

Accounting Policies [Abstract]

Summary of Common Stock Equivalents Outstanding


	As of March 31,
	2018		2017
Options to purchase common stock		5,839,261		4,048,377
Unvested restricted common stock		13,393		16,597

		5,852,654		4,064,974

Fair Value Measurements and Marketable Securities (Tables)

3 Months Ended

Mar. 31, 2018

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 March 31, 2018 and December 31, 2017:


	March 31, 2018
	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	$	28,311	$	28,311	$	—	$	—
Commercial paper		6,089		—		6,089		—
Corporate bonds		1,198		—		1,198		—

Total cash equivalents		35,598		28,311		7,287		—

Marketable securities:
Corporate bonds		27,214		—		27,214		—
Commercial paper		16,125		—		16,125		—

Total marketable securities		43,339		—		43,339		—

Total cash equivalents and marketable securities	$	78,937	$	28,311	$	50,626	$	—


	December 31, 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	$	15,802	$	15,802	$	—	$	—
Commercial paper		998		—		998		—
Corporate bonds		549		—		549		—

Total cash equivalents		17,349		15,802		1,547		—

Marketable securities:
Corporate bonds		50,844		—		50,844		—
Commercial paper		9,951		—		9,951		—
Certificates of deposit		480		—		480		—

Total marketable securities		61,275		—		61,275		—

Total cash equivalents and marketable securities	$	78,624	$	15,802	$	62,822	$	—

Summary of Marketable Securities

The following tables summarize the Company’s marketable securities as of March 31, 2018 and December 31, 2017:


	March 31, 2018
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
Assets:
Corporate bonds (due within 1 year)	$	27,250	$	—	$	(36	)	$	27,214
Commercial paper (due within 1 year)		16,136		—		(11	)		16,125

	$	43,386	$	—	$	(47	)	$	43,339


	December 31, 2017
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
Assets:
Corporate bonds (due within 1 year)	$	50,892	$	—	$	(48	)	$	50,844
Commercial paper (due within 1 year)		9,961		—		(10	)		9,951
Certificates of deposit (due within 1 year)		480		—		—			480

	$	61,333	$	—	$	(58	)	$	61,275

- 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)

3 Months Ended

Mar. 31, 2018

Payables and Accruals [Abstract]

Schedule of Accrued Expenses

Accrued expenses consisted of the following as of March 31, 2018 and December 31, 2017:


	March 31, 2018		December 31, 2017
	(in thousands)
Accrued research and development expenses	$	2,075	$	1,647
Accrued payroll and related expenses		836		2,229
Accrued professional fees		564		292
Accrued other		186		105

	$	3,661	$	4,273

Notes Payable (Tables)

3 Months Ended

Mar. 31, 2018

Debt Disclosure [Abstract]

Schedule of Estimated Future Principal Payments

As of March 31, 2018, the estimated future principal payments due are as follows:


Year Ending December 31,
(in thousands)
2018	$	—
2019		5,454
2020		7,273
2021		7,273

Total	$	20,000

Stock-Based Awards (Tables)

3 Months Ended

Mar. 31, 2018

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 March 31,
	2018		2017
	(in thousands)
Research and development	$	1,572	$	856
General and administrative		894		1,145

	$	2,466	$	2,001

Commitments and Contingencies (Tables)

3 Months Ended

Mar. 31, 2018

Commitments and Contingencies Disclosure [Abstract]

Schedule of Future Minimum Lease Payments for Operating Leases

Future minimum lease payments for its operating leases as of March 31, 2018 were as follows:


Year Ending December 31,
(in thousands)
2018 (April - December)	$	360
2019		464
2020		226
2021		—

	$	1,050

Nature of the Business and Basis of Presentation - Additional Information (Detail) - USD ($) $ in Thousands	3 Months Ended	148 Months Ended
	Mar. 31, 2018	Dec. 31, 2017	Dec. 29, 2017
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Entity incorporation date	Nov. 22, 2005
Accumulated deficit	$ (305,533)	$ (289,577)
Net proceeds from sale of securities		333,300
Total cash, cash equivalents and marketable securities	89,100
Term Loan [Member]
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Aggregate principal balance	20,000		$ 20,000
Loan agreement minimum liquidity required	$ 21,000	$ 21,000

Summary of Significant Accounting Policies - Summary of Common Stock Equivalents Outstanding (Detail) - shares	3 Months Ended
	Mar. 31, 2018	Mar. 31, 2017
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	5,852,654	4,064,974
Options to Purchase Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	5,839,261	4,048,377
Unvested Restricted Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	13,393	16,597

Fair Value Measurements and Marketable Securities - Summary of Cash Equivalents and Marketable Securities (Detail) - USD ($) $ in Thousands	Mar. 31, 2018	Dec. 31, 2017
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	$ 35,598	$ 17,349
Marketable securities	43,339	61,275
Total cash equivalents and marketable securities	78,937	78,624
Money Market Funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	28,311	15,802
Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	6,089	998
Marketable securities	16,125	9,951
Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	1,198	549
Marketable securities	27,214	50,844
Certificates of Deposit [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Marketable securities		480
Quoted Prices in Active Markets, (Level 1) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	28,311	15,802
Total cash equivalents and marketable securities	28,311	15,802
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	28,311	15,802
Significant Other Observable Inputs (Level 2) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	7,287	1,547
Marketable securities	43,339	61,275
Total cash equivalents and marketable securities	50,626	62,822
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	6,089	998
Marketable securities	16,125	9,951
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	1,198	549
Marketable securities	$ 27,214	50,844
Significant Other Observable Inputs (Level 2) [Member] \| Certificates of Deposit [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Marketable securities		$ 480

Fair Value Measurements and Marketable Securities - Summary of Marketable Securities (Detail) - USD ($) $ in Thousands	Mar. 31, 2018	Dec. 31, 2017
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 43,386	$ 61,333
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(47)	(58)
Fair Value	43,339	61,275
Corporate Bonds (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	27,250	50,892
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(36)	(48)
Fair Value	27,214	50,844
Commercial Paper (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	16,136	9,961
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(11)	(10)
Fair Value	$ 16,125	9,951
Certificates of Deposit (Due Within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost		480
Gross Unrealized Gains		0
Fair Value		$ 480

Accrued Expenses - Schedule of Accrued Expenses (Detail) - USD ($) $ in Thousands	Mar. 31, 2018	Dec. 31, 2017
Payables and Accruals [Abstract]
Accrued research and development expenses	$ 2,075	$ 1,647
Accrued payroll and related expenses	836	2,229
Accrued professional fees	564	292
Accrued other	186	105
Total accrued expense	$ 3,661	$ 4,273

Notes Payable - Additional Information (Detail) - USD ($)		3 Months Ended		12 Months Ended
	Dec. 29, 2017	Mar. 31, 2018	Mar. 31, 2017	Dec. 29, 2017	Dec. 31, 2017
Debt Instrument [Line Items]
Proceeds from issuance of notes payable	$ 20,000,000
Credit facility default amount		$ 300,000
Notes payable		20,200,000			$ 20,000,000
Maximum [Member]
Debt Instrument [Line Items]
Aggregate value of cash maintained by Australian subsidiary, limit		4,000,000
Term Loan [Member]
Debt Instrument [Line Items]
Maximum borrowings under term loan	$ 20,000,000	$ 20,000,000		$ 20,000,000
Debt facility description		Upon entering into this Term Loan, the Company is obligated to make monthly, interest-only payments until March 29, 2019 and, thereafter, to pay 33 consecutive, equal monthly installments of principal and interest from April 1, 2019 through December 1, 2021. The outstanding Term Loan bears a variable interest at an annual rate of 1.25% above the prime rate, which at March 31, 2018 was 4.75%. In addition, a final payment equal to 8.0% of the Term Loan is due upon the earlier of the maturity date, acceleration of the Term Loan or prepayment of all or part of the Term Loan.
Debt maturity date		Dec. 01, 2021
Debt facility interest rate description		1.25% above the prime rate
Debt facility interest rate		1.25%
Debt facility effective interest rate		4.75%
Debt facility fee percentage				8.00%
Charges to interest expense of debt outstanding				$ 1,600,000
Loan agreement minimum liquidity required		$ 21,000,000			$ 21,000,000
Debt facility covenant description		Further, as of 45 days after the Term Loan was entered in, the Company met its obligation to maintain a balance of unrestricted cash, cash equivalents and marketable securities at Silicon Valley Bank in an amount not less than the greater of (i) $55.0 million and (ii) sixty-five percent (65%) of all the Company’s cash, cash equivalents and marketable securities. If the Company does not meet this requirement it will not be considered an event of default provided it immediately secures 87.5% of the principal balance in a restricted cash account.
Interest expense on term loan		$ 500,000
Debt facility effective interest rate		9.20%
Term Loan [Member] \| Minimum [Member]
Debt Instrument [Line Items]
Percentage equivalent of cash, cash equivalents and marketable securities balance		105.00%
2014 Credit Facility [Member] \| Secured Debt [Member]
Debt Instrument [Line Items]
Debt facility effective interest rate			10.80%
Interest expense on credit facility			$ 100,000

Notes Payable - Schedule of Estimated Future Principal Payments (Detail) $ in Thousands	Mar. 31, 2018 USD ($)
Debt Instruments [Abstract]
2018	$ 0
2019	5,454
2020	7,273
2021	7,273
Total	$ 20,000

Stock-Based Awards - Additional Information (Detail) - 2014 Stock Option and Incentive Plan [Member] - shares	Jan. 01, 2018	Mar. 31, 2018
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for grant		1,677,858
Shares added to plan	1,099,578

Stock-Based Awards - Summary of Stock-Based Compensation Expense Related to Stock Options and Restricted Common Stock (Detail) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2018	Mar. 31, 2017
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 2,466	$ 2,001
Research and Development [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	1,572	856
General and Administrative [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 894	$ 1,145

Commitments and Contingencies - Additional Information (Detail)					1 Months Ended	3 Months Ended
	Jan. 01, 2017 ft²	Oct. 01, 2015	Apr. 15, 2015 Option	Jul. 28, 2014	Jan. 31, 2017	Mar. 31, 2018 USD ($)	Mar. 31, 2017 USD ($)
Other Commitments [Line Items]
Operating lease, rental expense						$ 100,000	$ 100,000
Subsequent Licensed Product [Member]
Other Commitments [Line Items]
Licensing fees per product maximum						1,300,000
Development Based Milestones [Member]
Other Commitments [Line Items]
Milestone payments due						$ 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
Boston Office Space [Member] \| Unrelated Third Party Member
Other Commitments [Line Items]
Subleased area \| ft²	2,976
Sublease expiration date	Dec. 31, 2018
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
Maximum [Member] \| Product Commercialization Milestones [Member]
Other Commitments [Line Items]
Milestone payments						$ 12,500,000

Commitments and Contingencies - Schedule of Future Minimum Lease Payments for Operating Leases (Detail) $ in Thousands	Mar. 31, 2018 USD ($)
Commitments and Contingencies Disclosure [Abstract]
2018 (April - December)	$ 360
2019	464
2020	226
2021	0
Total	$ 1,050

Retirement Plan - Additional Information (Detail) - USD ($) $ in Millions	3 Months Ended		12 Months Ended
	Mar. 31, 2018	Mar. 31, 2017	Dec. 31, 2017
Defined Contribution Plan Disclosure [Line Items]
Percentage of employer's contribution on employee's base salary			3.00%
Retirement 401K Plan [Member]
Defined Contribution Plan Disclosure [Line Items]
Contribution expense	$ 0.1
SIMPLE IRA plan [Member] \| Maximum [Member]
Defined Contribution Plan Disclosure [Line Items]
Contribution expense		$ 0.1

Australia Research and Development Tax Incentive - Additional Information (Detail) - USD ($)	3 Months Ended
	Mar. 31, 2018	Mar. 31, 2017	Dec. 31, 2017
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency transaction gains (losses)	$ (14,000)	$ 21,000
Research and Development [Member]
Research and Development Tax Incentive [Line Items]
Percentage of reduction in research and development costs	43.50%
Zafgen Australia Pty Limited [Member] \| Australia [Member]
Research and Development Tax Incentive [Line Items]
Tax incentive receivable	$ 1,500,000		$ 900,000
Zafgen Australia Pty Limited [Member] \| Research and Development [Member]
Research and Development Tax Incentive [Line Items]
Percentage of refundable tax incentive	43.50%
Reduction to research and development expenses	$ 600,000	0
Zafgen Australia Pty Limited [Member] \| Maximum [Member]
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency transaction gains (losses)	$ 100,000	$ 100,000