Amyris (AMRSQ) 10-Q5 Nov 132013 Q3 Quarterly reportFinancial data

Company Profile

Document_and_Entity_Informatio

Document and Entity Information	9 Months Ended
Document and Entity Information	Sep. 30, 2013	Oct. 31, 2013
Document Information [Line Items]	'	'
Entity Registrant Name	'AMYRIS, INC.	'
Entity Central Index Key	'0001365916	'
Current Fiscal Year End Date	'--12-31	'
Entity Filer Category	'Accelerated Filer	'
Document Type	'10-Q	'
Document Period End Date	30-Sep-13	'
Document Fiscal Year Focus	'2013	'
Document Fiscal Period Focus	'Q3	'
Amendment Flag	'false	'
Entity Common Stock, Shares Outstanding	'	76,270,980

Condensed_Consolidated_Balance

Condensed Consolidated Balance Sheets (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified	Sep. 30, 2013	Dec. 31, 2012
Current assets:	'	'
Cash and cash equivalents	$5,756	$30,592
Short-term investments	580	97
Accounts receivable, net of allowance of $481 as of September 30, 2013 and December 31, 2012	2,789	3,846
Related party accounts receivable	1,022	0
Inventories, net	7,948	6,034
Prepaid expenses and other current assets	7,164	8,925
Total current assets	25,259	49,494
Property, plant and equipment, net	140,718	163,121
Restricted cash	956	955
Other assets	19,725	20,112
Goodwill and intangible assets	9,120	9,152
Total assets	195,778	242,834
Current liabilities:	'	'
Accounts payable	12,881	15,392
Deferred revenue	7,351	1,333
Accrued and other current liabilities	20,305	24,410
Capital lease obligation, current portion	1,031	1,366
Debt, current portion	5,448	3,325
Total current liabilities	47,016	45,826
Capital lease obligation, net of current portion	464	1,244
Long-term debt, net of current portion	55,299	61,806
Related party debt	58,091	39,033
Deferred rent, net of current portion	10,084	8,508
Deferred revenue, net of current portion	5,000	4,255
Other liabilities	19,404	15,933
Total liabilities	195,358	176,605
Commitments and contingencies (Note 5)	'	'
Stockholdersâ€™ equity:	'	'
Preferred stock - $0.0001 par value, 5,000,000 shares authorized, none issued and outstanding	0	0
Common stock - $0.0001 par value, 200,000,000 and 100,000,000 shares authorized as of September 30, 2013 and December 31, 2012, respectively; 76,245,375 and 68,709,660 shares issued and outstanding as of September 30, 2013 and December 31, 2012, respectively	8	7
Additional paid-in capital	699,979	666,233
Accumulated other comprehensive loss	-16,961	-12,807
Accumulated deficit	-682,016	-586,327
Total Amyris, Inc. stockholdersâ€™ equity	1,010	67,106
Noncontrolling interest	-590	-877
Total stockholders' equity	420	66,229
Total liabilities and stockholders' equity	$195,778	$242,834

Condensed_Consolidated_Balance1

Condensed Consolidated Balance Sheets (Parentheticals) (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, except Share data, unless otherwise specified	Sep. 30, 2013	Dec. 31, 2012
Allowance for Doubtful Accounts	$481	$481
Stockholders' Equity:	'	'
Preferred stock, par value	$0.00	$0.00
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	$0.00	$0.00
Common stock, shares authorized	200,000,000	100,000,000
Common stock, shares issued	76,245,375	68,709,660
Common Stock, Shares, Outstanding	76,245,375	68,709,660

Condensed_Consolidated_Stateme

Condensed Consolidated Statements of Operations (USD $)	3 Months Ended		9 Months Ended
In Thousands, except Share data, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Revenues	'	'	'	'
Product sales	$3,138	$4,728	$10,130	$46,615
Related party product sales	1,006	0	1,182	0
Total product sales	4,144	4,728	11,312	46,615
Grants and collaborations revenue	2,860	4,605	11,763	11,450
Related party grants and collaborations revenue	0	9,775	2,647	9,775
Total grants and collaborations revenue	2,860	14,380	14,410	21,225
Total revenues	7,004	19,108	25,722	67,840
Cost and operating expenses	'	'	'	'
Cost of products sold	8,328	4,444	26,141	71,891
Loss on purchase commitments and write off of production assets	0	1,438	8,423	38,090
Research and development	13,370	15,736	43,116	55,580
Sales, general and administrative	13,057	17,355	42,602	61,301
Total cost and operating expenses	34,755	38,973	120,282	226,862
Loss from operations	-27,751	-19,865	-94,560	-159,022
Other income (expense):	'	'	'	'
Interest income	21	297	114	1,406
Interest expense	-2,110	-1,224	-5,230	-3,538
Other income (expense), net	4,177	664	3,266	-512
Total other income (expense)	2,088	-263	-1,850	-2,644
Loss before income taxes	-25,663	-20,128	-96,410	-161,666
Benefit (provision) for income taxes	1,435	-260	953	-753
Net loss	-24,228	-20,388	-95,457	-162,419
Net (income) loss attributable to noncontrolling interest	29	95	-232	772
Net loss attributable to Amyris, Inc. common stockholders	($24,199)	($20,293)	($95,689)	($161,647)
Net loss per share attributable to common stockholders, basic and diluted (in dollars per share)	($0.32)	($0.34)	($1.27)	($2.91)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	76,205,853	58,964,226	75,167,877	55,552,949

Condensed_Consolidated_Stateme1

Condensed Consolidated Statements of Comprehensive Loss (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Net loss	($24,228)	($20,388)	($95,457)	($162,419)
Foreign currency translation adjustment, net of tax	-66	-410	-4,099	-6,346
Total comprehensive loss	-24,294	-20,798	-99,556	-168,765
Net (income) loss attributable to noncontrolling interest	29	95	-232	772
Foreign currency translation adjustment attributable to noncontrolling interest	-3	-41	-55	-209
Comprehensive loss attributable to Amyris, Inc.	($24,268)	($20,744)	($99,843)	($168,202)

Condensed_Consolidated_Stateme2

Condensed Consolidated Statements Stockholders' Equity (USD $)	Total	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Deficit [Member]	Accumulated Other Comprehensive Income (Loss) [Member]	Noncontrolling Interest [Member]
In Thousands, except Share data, unless otherwise specified	Total	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Deficit [Member]	Accumulated Other Comprehensive Income (Loss) [Member]	Noncontrolling Interest [Member]
Beginning Balance, value at Dec. 31, 2012	$66,229	$7	$666,233	($586,327)	($12,807)	($877)
Beginning Balance, shares at Dec. 31, 2012	68,709,660	68,709,660	'	'	'	'
Increase (Decrease) in Stockholders' Equity [Roll Forward]	'	'	'	'	'	'
Issuance of common stock upon exercise of stock options, net of restricted stock, value	747	'	747	'	'	'
Issuance of common stock upon exercise of stock options, net of restricted stock, shares	'	510,107	'	'	'	'
Stock issued during period	19,979	1	19,978	'	'	'
Stock issued during period, shares	'	6,567,299	'	'	'	'
Shares issued from restricted stock unit settlement, value	-590	'	-590	'	'	'
Shares issued from restricted stock unit settlement, shares	'	458,309	'	'	'	'
Stock-based compensation	13,611	'	13,611	'	'	'
Foreign currency translation adjustment, net of tax	-4,099	'	'	'	-4,154	55
Net income (loss)	-95,457	'	'	-95,689	'	232
Ending Balance, value at Sep. 30, 2013	$420	$8	$699,979	($682,016)	($16,961)	($590)
Ending Balance, shares at Sep. 30, 2013	76,245,375	76,245,375	'	'	'	'

Condensed_Consolidated_Stateme3

Condensed Consolidated Statements Stockholders' Equity Condensed Consolidated Statements Stockholders' Equity (Parenthetical) (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013
Statement of Stockholders' Equity [Abstract]	'
Payments of Stock Issuance Costs	$21

Consolidated_Statements_of_Cas

Consolidated Statements of Cash Flows (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012
Operating activities	'	'
Net loss	($95,457)	($162,419)
Adjustments to reconcile net loss to net cash used in operating activities:	'	'
Depreciation and amortization	12,259	10,686
Loss on disposal of property, plant and equipment	81	208
Stock-based compensation	13,611	21,400
Amortization of debt discount	2,135	316
Provision for doubtful accounts	0	236
Loss on purchase commitments and write off of production assets	8,423	38,090
Change in fair value of derivative instruments	-5,295	364
Other noncash expenses	213	108
Changes in assets and liabilities:	'	'
Accounts receivable	1,390	2,864
Related party accounts receivable	-1,022	0
Inventories, net	-2,590	612
Prepaid expenses and other assets	-1,477	10,655
Accounts payable	2,848	-11,200
Accrued, other current liabilities and other liabilities	-10,966	-29,362
Deferred revenue	6,763	-1,308
Deferred rent	-340	-943
Net cash used in operating activities	-69,424	-119,693
Investing activities	'	'
Purchase of short-term investments	-1,820	-8,240
Maturities of short-term investments	1,209	0
Sales of short-term investments	0	16,449
Change in restricted cash	-1	-954
Purchase of property, plant and equipment, net of disposals	-5,901	-50,344
Deposits on property, plant and equipment	0	-562
Net cash used in investing activities	-6,513	-43,651
Financing activities	'	'
Proceeds from issuance of common stock, net of repurchases	157	696
Proceeds from issuance of common stock in private placements, net of issuance costs	19,981	62,490
Principal payments on capital leases	-1,115	-2,970
Proceeds from debt issued	2,709	75,624
Proceeds from debt issued to related party	30,000	30,000
Principal payments on debt	-2,494	-52,052
Net cash provided by financing activities	49,238	113,788
Effect of exchange rate changes on cash and cash equivalents	1,863	-1,774
Net decrease in cash and cash equivalents	-24,836	-51,330
Cash and cash equivalents at beginning of period	30,592	95,703
Cash and cash equivalents at end of period	5,756	44,373
Supplemental disclosures of cash flow information:	'	'
Cash paid for interest	1,610	2,831
Cash paid for income taxes, net of refunds	0	0
Supplemental disclosures of noncash investing and financing activities:	'	'
Acquisitions of property, plant and equipment within accounts payable, accrued liabilities and notes payable	1,444	5,672
Financing of insurance premium under notes payable	43	0
Long-term deposits used for purchase of property, plant and equipment	$0	$12,286

The_Company

The Company	9 Months Ended
The Company	Sep. 30, 2013
The Company [Abstract]	'
The Company	'
	The Company

	Amyris, Inc. (the “Company”) was incorporated in California on July 17, 2003 and reincorporated in Delaware on June 10, 2010 for the purpose of leveraging breakthroughs in synthetic biology to develop and provide renewable compounds for a variety of markets. The Company is currently building and applying its industrial synthetic biology platform to provide alternatives to select petroleum-sourced products used in specialty chemical and transportation fuel markets worldwide. The Company's first commercialization efforts have been focused on a renewable hydrocarbon molecule called farnesene ("Biofene®"), which forms the basis for a wide range of products varying from specialty chemical applications to transportation fuels, such as diesel. While the Company's platform is able to use a wide variety of feedstocks, the Company is focused initially on Brazilian sugarcane. In addition, the Company has entered into various contract manufacturing agreements to support commercial production. The Company has established two principal operating subsidiaries, Amyris Brasil Ltda. (formerly Amyris Brasil S.A., “Amyris Brasil”) for production in Brazil, and Amyris Fuels, LLC ("Amyris Fuels"). Nearly all of the Company's revenues through 2012 came from the sale of ethanol and reformulated ethanol-blended gasoline with substantially all of the remaining revenues coming from collaborations, government grants and sales of renewable products. In the third quarter of 2012, the Company transitioned out of the ethanol and reformulated ethanol-blended gasoline business. The Company does not expect to be able to replace much of the revenue lost in the near term as a result of this transition, particularly in 2013, while it continues its efforts to establish a renewable products business.

	The Company's renewable products business strategy is to focus on the commercialization of specialty products while moving established commodity products into joint venture arrangements with leading industry partners. To commercialize its products, the Company must be successful in using its technology to manufacture its products at commercial scale and on an economically viable basis (i.e., low per unit production costs). The Company is building experience producing renewable products at commercial scale. The Company's prospects are subject to risks, expenses and uncertainties frequently encountered by companies in this stage of development.

	The Company expects to fund its operations for the foreseeable future with cash and investments currently on hand, with cash inflows from collaboration and grant funding, cash contributions from product sales, and with new debt and equity financings. The Company's planned 2013 and 2014 working capital needs and its planned operating and capital expenditures for 2013 and 2014 are dependent on significant inflows of cash from existing collaboration partners and from funds under existing convertible debt facility, as well as additional funding from new collaborations, and may also require additional funding from credit facilities or loans. The Company will continue to need to fund its research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of its business. The Company's operating plan contemplates capital expenditures of approximately $10.0 million in 2013 and the Company expects to continue to incur costs in connection with its existing contract manufacturing arrangements (see Note 6, "Debt" and Note 10, "Stockholders' Equity").

	Liquidity

	The Company has incurred significant losses since its inception and believes that it will continue to incur losses and negative cash flow from operations into at least 2014. As of September 30, 2013, the Company had an accumulated deficit of $682.0 million and had cash, cash equivalents and short term investments of $6.3 million. The Company has significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of September 30, 2013, the Company's debt, net of debt discount, totaled $118.8 million, of which $5.4 million matures within the next twelve months. In addition, the Company's debt agreements contain various covenants, including restrictions on the Company's business that could cause the Company to be at risk of defaults. Please refer to Note 5, "Commitments and Contingencies" and Note 6, "Debt" for further details regarding the Company's obligations and commitments.

	In August 2013, the Company entered into a purchase agreement with Total Energies Nouvelles Activités USA (f.k.a. Total Gas & Power USA SAS) ("Total") and Maxwell (Mauritius) Pte Ltd (“Temasek”) to sell up to $73.0 million in convertible promissory notes in private placements, with such notes to be sold and issued over a period of up to 24 months from the date of signing (the "August 2013 Financing"). The purchase agreement provided for the financing to be divided into two tranches (the first tranche for $42.6 million and the second tranche for $30.4 million), each with differing closing conditions. Of the total possible purchase price in the financing, $60.0 million was contemplated to be paid in the form of cash by Temasek ($35.0 million in the first tranche and up to $25.0 million in the second tranche) and $13.0 million was contemplated to be paid by exchange and cancellation of outstanding convertible promissory notes by Total in connection with its exercise of pro rata rights ($7.6 million in the first tranche and up to $5.4 million in the second tranche). In October 2013, the Company amended the financing agreement to include an additional investor in the first tranche convertible promissory notes in the principal amount of $7.6 million in additional cash funding, and to proportionally increase the amount acquired by exchange and cancellation of outstanding convertible promissory notes by Total in connection with its exercise of pro rata rights to $14.6 million ($9.2 million in the first tranche and up to $5.4 million in the second tranche). Also in October 2013, the Company completed the closing of the first tranche of the August 2013 Financing, issuing a total of $51.8 million in convertible promissory notes for cash proceeds of $7.6 million and cancellation of outstanding promissory notes and convertible promissory notes of $44.2 million, of which $35.0 million resulted from the cancellation of the Temasek Bridge Note (as defined below and as described further under Note 17, "Subsequent Events").

	In September 2013, the Company entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million as needed before the initial closing of the August 2013 Financing. The bridge loan agreement provided for the sale of up to $5.0 million in principal amount of unsecured convertible promissory notes at any time prior to October 31, 2013 following the satisfaction of certain closing conditions, including a condition that the Company pay an availability fee for the bridge loan. The Company did not use this facility and it expired in October 2013 in accordance with its terms.

	In October 2013, the Company sold and issued a senior secured promissory note to Temasek for a bridge loan of $35.0 million (the "Temasek Bridge Note"). The note was due on February 2, 2014 and accrued interest at a rate of 5.5% each four months from October 4, 2013. On October 16, 2013, the note was cancelled as payment for the investor’s purchase of a first tranche convertible promissory note in aggregate principal amount of $35.0 million in the August 2013 Financing. All interest outstanding under the Temasek Bridge Note at the time of cancellation was transferred to the first tranche convertible promissory note.

	In addition to cash contributions from product sales and debt and equity financings, the Company also depends on collaboration funding to support its operating expenses. While part of this funding is committed based on existing collaboration agreements, the Company will need to identify and obtain funding under additional collaborations that are not yet subject to any definitive agreement or are not yet identified. In addition, some of the Company’s existing collaboration funding is subject to achievement by the Company of milestones or other funding conditions.

	If the Company cannot secure sufficient collaboration funding to support its operating expenses in excess of cash contributions from product sales and existing debt and equity financings, it may need to issue additional preferred and/or discounted equity, agree to onerous covenants, grant further security interest in its assets, enter into collaboration and licensing arrangements that require it to relinquish commercial rights, or grant licenses on terms that are not favorable. If the Company fails to secure such funding, the Company could be forced to curtail its operations, which would have a material adverse effect on the Company's ability to continue with its business plans, and the Company's status as a going concern.

Summary_of_Significant_Account

Summary of Significant Accounting Policies	9 Months Ended
Summary of Significant Accounting Policies	Sep. 30, 2013
Accounting Policies [Abstract]	'
Summary of Significant Accounting Policies	'
	Summary of Significant Accounting Policies

	Basis of Presentation

	The accompanying interim condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (“GAAP”) and with the instructions for Form 10-Q and Regulation S-X. Accordingly, they do not include all of the information and notes required for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Form 10-K filed with the Securities and Exchange Commission (“SEC”) on March 28, 2013. The unaudited condensed consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

	Use of Estimates

	In preparing the unaudited condensed consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the unaudited condensed consolidated financial statements and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.

	Unaudited Interim Financial Information

	The accompanying interim condensed consolidated financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual consolidated financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the results of operations for the periods presented. The year-end condensed consolidated balance sheet data was derived from audited financial statements, but does not include all disclosures required by GAAP. The condensed consolidated results of operations for any interim period are not necessarily indicative of the results to be expected for the full year or for any other future year or interim period.

	Recent Accounting Pronouncements

	In December 2011, the International Accounting Standards Board and the Financial Accounting Standards Board ("FASB") issued common disclosure requirements that are intended to enhance comparability between financial statements prepared on the basis of GAAP and those prepared in accordance with International Financial Reporting Standards. In January 2013, the FASB issued an accounting standard update to limit the scope of the new balance sheet offsetting disclosures to derivative instruments, repurchase agreements, and securities lending transactions to the extent that they are offset in the financial statement or subject to an enforceable master netting arrangement or similar arrangement. While this guidance does not change existing offsetting criteria in GAAP or the permitted balance sheet presentation for items meeting the criteria, it requires an entity to disclose both net and gross information about assets and liabilities that have been offset and the related arrangements. Required disclosures under this new guidance should be provided retrospectively for all comparative periods presented. This new guidance is effective for fiscal years beginning on or after January 1, 2013, and interim periods within those years. The adoption of this guidance in the Company's first quarter of fiscal year 2013 did not have a material effect on the Company's consolidated financial statements.

	In July 2012, the FASB issued an amended accounting standard update to simplify how entities test indefinite-lived intangible assets for impairment which improve consistency in impairment testing requirements among long-lived asset categories. The amended guidance permits an assessment of qualitative factors to determine whether it is more likely than not that the fair value of an indefinite-lived intangible asset is less than its carrying value. For assets in which this assessment concludes it is more likely than not that the fair value is more than its carrying value, then the amended guidance eliminates the requirement to perform quantitative impairment testing as outlined in the previously issued standards. The amended guidance is effective for fiscal years beginning after September 15, 2012 and early adoption is permitted. The adopted and amended guidance did not have an impact on the Company's consolidated financial statements.

	In February 2013, in connection with the accounting standard related to the presentation of the statement of comprehensive income, the FASB issued an accounting standard update to improve the reporting of reclassifications out of accumulated other comprehensive income of various components. This guidance requires companies to present either parenthetically on the face of the financial statements or in the notes, significant amounts reclassified from each component of accumulated other comprehensive income and the income statement line items affected by the reclassification. This standard is effective for interim periods and fiscal years beginning after December 15, 2012. The adoption of this guidance in the Company's first quarter of fiscal year 2013 did not have a material effect on the Company's consolidated financial statements.

	In July 2013, the FASB issued a new accounting standard update on the financial statement presentation of unrecognized tax benefits. The new guidance provides that a liability related to an unrecognized tax benefit would be presented as a reduction of a deferred tax asset for a net operating loss carryforward, a similar tax loss or a tax credit carryforward if such settlement is required or expected in the event the uncertain tax position is disallowed. The new guidance becomes effective for the Company on January 1, 2014 and will be applied prospectively to unrecognized tax benefits that exist at the effective date with retrospective applications permitted. The Company is currently assessing the impact of this new guidance.

Fair_Value_of_Financial_Instru

Fair Value of Financial Instruments	9 Months Ended
	Sep. 30, 2013
Fair Value Disclosures [Abstract]	'
Fair Value of Financial Instruments	'
	Fair Value of Financial Instruments

	The inputs to the valuation techniques used to measure fair value are classified into the following categories:

	Level 1: Quoted market prices in active markets for identical assets or liabilities.

	Level 2: Observable market-based inputs or unobservable inputs that are corroborated by market data.

	Level 3: Unobservable inputs that are not corroborated by market data.

	As of September 30, 2013, the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):


		Level 1				Level 2				Level 3				Balance as of
														30-Sep-13
	Financial Assets
	Money market funds	$	245			$	—			$	—			$	245

	Certificates of deposit	580				—				—				580

	Total financial assets	$	825			$	—			$	—			$	825

	Financial Liabilities
	Loans payable(1)	$	—			$	19,502			$	—			$	19,502

	Credit facilities(1)	—				8,555				—				8,555

	Convertible notes(1)	—				—				88,261				88,261

	Compound embedded derivative liability	—				—				13,836				13,836

	Currency interest rate swap derivative liability	—				3,074				—				3,074

	Total financial liabilities	$	—			$	31,131			$	102,097			$	133,228


	______________
	(1) These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis.

	The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The fair values of money market funds are based on fair values of identical assets. The fair values of the loans payable, convertible notes, credit facilities and currency interest rate swaps are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company. Market risk associated with fixed and variable rate long-term debt relates to the potential reduction in fair value and negative impact to future earnings, respectively, from an increase in interest rates.

	The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, accounts payable, accrued liabilities and notes payable, approximate fair value due to their relatively short maturities, and low market interest rates, if applicable. The fair values of the loans payable, convertible notes and credit facilities are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company.

	The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liability measured at fair value using significant unobservable inputs (Level 3) (in thousands):


		Compound Embedded Derivative Liability
	Balance at December 31, 2012	$	7,894

	Transfers in to Level 3	13,076

	Total (gain) losses included in other income (expense), net	(7,134		)
	Balance at September 30, 2013	$	13,836


	The compound embedded derivative liability, which is included in other liabilities, represents the fair value of the equity conversion option and a "make-whole" provision relating to the outstanding senior unsecured convertible promissory notes issued to Total (see Note 6, "Debt"). There is no current observable market for this type of derivative and, as such, the Company determined the fair value of the embedded derivative using a Black-Scholes valuation model that combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of the Company's common stock into which the notes are convertible. The Company marks the compound embedded derivative to market due to the conversion price not being indexed to the Company's own stock. Except for the "make-whole" provision included in the conversion option, which is only required to be settled in cash upon a change of control at the noteholder's option, the compound embedded derivative will be settled in either cash or shares. As of September 30, 2013, the Company has sufficient common stock available to settle the conversion option in shares.

	The Company’s financial assets and financial liabilities as of December 31, 2012 are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):



		Level 1				Level 2				Level 3				Balance as of December 31, 2012
	Financial Assets
Money market funds	$	15,847			$	—			$	—			$	15,847

Certificates of deposit	757				—				—				757

Total financial assets	$	16,604			$	—			$	—			$	16,604

Financial Liabilities
Notes payable(1)	$	—			$	1,676			$	—			$	1,676

Loans payable(1)	—				20,707				—				20,707

Credit facilities(1)	—				11,503				—				11,503

Convertible notes(1)	—				—				62,522				62,522

Compound embedded derivative liability	—				—				7,894				7,894

Currency interest rate swap derivative liability	—				1,367				—				1,367

Total financial liabilities	$	—			$	35,253			$	70,416			$	105,669


______________
(1) These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis.

Derivative Instruments

The Company’s derivative instruments included Chicago Board of Trade ethanol futures and Reformulated Blendstock for Oxygenate Blending gasoline futures. All derivative commodity instruments were recorded at fair value on the condensed consolidated balance sheets. None of the Company’s derivative instruments were designated as hedging instruments. Changes in the fair value of these non-designated hedging instruments were recognized in cost of products sold in the condensed consolidated statements of operations. As of September 30, 2013, the Company had no outstanding derivative commodity instruments resulting from the Company's transition out of its ethanol and ethanol-blended gasoline business in the quarter ended September 30, 2012.

In June 2012, the Company entered into a loan agreement with Banco Pine S.A. ("Banco Pine") under which Banco Pine provided the Company with a short term loan of R$52.0 million (approximately US$25.6 million based on the exchange rate as of September 30, 2012, the time of the loan repayment) (the “Banco Pine Bridge Loan”). At the time of the Banco Pine Bridge Loan, the Company also entered into a currency interest rate swap arrangement with Banco Pine with respect to the repayment of R$22.0 million (approximately US$9.9 million based on the exchange rate of as of September 30, 2013). The swap arrangement exchanges the principal and interest payments under the Banco Pine loan of R$22.0 million entered into in July 2012 (the "Banco Pine Loan") for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of 3.94%. Changes in the fair value of the swap are recognized in other income (expense), net in the condensed consolidated statements of operations.

As of September 30, 2013, included in Other Liabilities on the condensed consolidated balance sheet is the Company's compound embedded derivative liability of $13.8 million, which represents the fair value of the equity conversion option and "make-whole" provision relating to the outstanding senior unsecured convertible promissory notes issued to Total as described above.

Derivative instruments measured at fair value as of September 30, 2013 and December 31, 2012, and their classification on the condensed consolidated balance sheet and condensed consolidated statements of operations, are presented in the following tables (in thousands except contract amounts):


		Asset/Liability as of
		30-Sep-13							31-Dec-12
Type of Derivative Contract		Quantity of			Fair Value				Quantity of			Fair Value
		Contracts							Contracts
Currency interest rate swap, included as net liability in other liabilities		1			$	3,074			1			$	1,367




Type of Derivative Contract		Income	Three Months Ended September 30,								Nine Months Ended September 30,
		Statement Classification	2013				2012				2013				2012
			Gain (Loss) Recognized								Gain (Loss) Recognized
Regulated fixed price futures contracts		Cost of products sold	$	—			$	(31	)		$	—			$	(288	)

Currency interest rate swap		Other income (expense), net	$	(137	)		$	82			$	(1,707	)		$	(1,133	)

Balance_Sheet_Components

Balance Sheet Components	9 Months Ended
	Sep. 30, 2013
Balance Sheet Components [Abstract]	'
Balance Sheet Components	'
	Balance Sheet Components

	Inventories

	Inventories are stated at the lower of cost or market and consist of the following (in thousands):


		September 30,				December 31,
		2013				2012
	Raw materials	$	1,527			$	1,574

	Work-in-process	5,218				1,771

	Finished goods	1,203				2,689

	Inventories, net	$	7,948			$	6,034


	The Company evaluates the recoverability of its inventories based on assumptions about expected demand and net realizable value. If the Company determines that the cost of inventories exceeds its estimated net realizable value, the Company records a write-down equal to the difference between the cost of inventories and the estimated net realizable value. Cost is computed on a first-in, first-out basis. Inventory costs include transportation costs incurred in bringing the inventory to its existing location. The Company also evaluates the terms of its agreements with its suppliers and establishes accruals for estimated adverse purchase commitments as necessary, applying the same lower of cost or market approach that is used to value inventory.

	Prepaid and Other Current Assets

	Prepaid and other current assets is comprised of the following (in thousands):


		September 30,				December 31,
		2013				2012
	Advances to contract manufacturers(1)	$	10			$	784

	Manufacturing catalysts	1,441				1,895

	Recoverable VAT and other taxes	4,146				4,167

	Other	1,567				2,079

	Prepaid and other current assets	$	7,164			$	8,925

	____

	-1	At December 31, 2012, the amount of $0.8 million, relates to the current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization was offset against purchases of inventory during 2013.

	Property, Plant and Equipment, net

	Property, plant and equipment, net is comprised of the following (in thousands):


				September 30,				December 31,
		Useful Life		2013				2012
	Leasehold improvements	Lesser of remaining useful life or lease term		$	39,114			$	39,290

	Machinery and equipment	7 - 15 Years		98,350				105,162

	Computers and software	3 - 5 Years		8,509				8,232

	Furniture and office equipment	5 years		2,520				2,467

	Buildings	15 Years		6,829				5,888

	Vehicles	5 years		465				575

	Construction in progress			42,933				45,372

				198,720				206,986

Less: accumulated depreciation and amortization			(58,002		)		(43,865		)
Property, plant and equipment, net			$	140,718			$	163,121


The Company's first, purpose-built, large-scale Biofene production plant in southeastern Brazil commenced operations in December 2012. This plant is located at Brotas in the state of São Paulo, Brazil and is adjacent to an existing sugar and ethanol mill, Paraíso Bioenergia. The Company's construction in progress consists primarily of the upfront plant design and the initial construction of a second large-scale production plant in Brazil, located at the Usina São Martinho sugar and ethanol mill (also in the state of São Paulo, Brazil).

Property, plant and equipment, net includes $3.4 million and $9.1 million of machinery and equipment and furniture and office equipment under capital leases as of September 30, 2013 and December 31, 2012, respectively. Accumulated amortization of assets under capital leases totaled $1.3 million and $4.1 million as of September 30, 2013 and December 31, 2012, respectively.

Depreciation and amortization expense, including amortization of assets under capital leases, was $3.8 million and $3.1 million for the three months ended September 30, 2013 and 2012, respectively, and was $12.2 million and $10.4 million for the nine months ended September 30, 2013 and 2012, respectively.

The Company capitalizes interest costs incurred to construct plant and equipment. The capitalized interest is recorded as part of the depreciable cost of the asset to which it relates to and is amortized over the asset's estimated useful life. Interest cost capitalized as of September 30, 2013 and December 31, 2012 was R$1.1 million (approximately $0.5 million and $0.6 million based on the exchange rates as of September 30, 2013 and December 31, 2012, respectively).

Other Assets

Other assets are comprised of the following (in thousands):


	September 30,				December 31,
	2013				2012

Deposits on property and equipment, including taxes	$	2,137			$	2,363

Advances to contract manufacturers, net of current portion(1)	—				2,222

Recoverable taxes on purchased property, plant and equipment and inventory(2)	15,609				13,597

Other	1,979				1,930

Total other assets	$	19,725			$	20,112

_________

(1)	At December 31, 2012, the amount of $2.2 million relates to the non-current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization was offset against purchases of inventory during 2013.

(2)	At September 30, 2013 and December 31, 2012, the amounts of $15.6 million and $13.6 million, respectively, are recoverable taxes from Brazilian governmental entities.

Accrued and Other Current Liabilities

Accrued and other current liabilities are comprised of the following (in thousands):


	September 30,				December 31,
	2013				2012

Professional services	$	2,859			$	824

Accrued vacation	2,179				2,673

Payroll and related expenses	5,099				5,809

Tax-related liabilities	641				851

Deferred rent, current portion	1,111				1,448

Accrued interest(1)	1,435				965

Contractual obligations to contract manufacturers, current	5,868				9,952

Customer advances	372				970

Other(1)	741				918

Total accrued and other current liabilities	$	20,305			$	24,410

__________

(1)	Certain reclassifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Other Liabilities

Other liabilities are comprised of the following (in thousands):


	September 30,				December 31,
	2013				2012
Contractual obligations to contract manufacturers, non-current	$	1,000			$	4,000

Fair market value of swap obligations	3,074				1,367

Fair value of compound embedded derivative liability(1)	13,836				7,894

Tax-related liabilities(2)	469				1,609

Other(2)	1,025				1,063

Total other liabilities	$	19,404			$	15,933

__________

(1)	The compound embedded derivative liability represents the fair value of the equity conversion feature and a "make-whole" feature related to the outstanding senior unsecured convertible promissory notes issued to Total.

(2)	Certain reclassifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Commitments_and_Contingencies

Commitments and Contingencies	9 Months Ended
	Sep. 30, 2013
Commitments and Contingencies Disclosure [Abstract]	'
Commitments and Contingencies	'
	Commitments and Contingencies

	The Company leases certain facilities and finances certain equipment under operating and capital leases. Operating leases include leased facilities and capital leases include leased equipment (see Note 4, "Balance Sheet Components"). Rent expense under operating leases was approximately $1.4 million and $1.2 million, respectively, for the three months ended September 30, 2013 and 2012, respectively, and was $3.5 million and $3.7 million for the nine months ended September 30, 2013 and 2012, respectively.

	In April 2013, the Company entered into an amendment to its operating lease for its headquarters in Emeryville, California (the "Amendment"). The Amendment provided for an extension of the lease term to May 2023, a modification of the base rent and elimination of the Company's loans and notes payable to the lessor of approximately $1.6 million (see Note 6, "Debt"). In addition, per the terms of the Amendment, the Company also received a rent credit of approximately $71,000 per month for the period of June 2013 through December 2013 and a rent credit of approximately $42,000 per month for the full year of 2014.

	Future minimum payments under the Company's lease obligations as of September 30, 2013, are as follows (in thousands):



	Years ending December 31:	Capital			Operating		Total Lease Obligations
		Leases			Leases
	2013 (Remaining Three Months)	$	274		$	1,477	$	1,751

	2014	1,007			6,277		7,284

	2015	289			6,581		6,870

	2016	—			6,595		6,595

	2017	—			6,585		6,585

	Thereafter	—			38,973		38,973

	Total future minimum lease payments	1,570			$	66,488	$	68,058

	Less: amount representing interest	(75		)

	Present value of minimum lease payments	1,495

	Less: current portion	(1,031		)

	Long-term portion	$	464


	Guarantor Arrangements

	The Company has agreements whereby it indemnifies its officers and directors for certain events or occurrences while the officer or director is, or was, serving at the Company’s request in such capacity. The term of the indemnification period is for the officer's or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer insurance policy that limits its exposure and enables the Company to recover a portion of any future amounts paid. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of September 30, 2013 and December 31, 2012.

	The Company has a credit facility with Financiadora de Estudos e Projetos (“FINEP”), a state-owned company subordinated to the Brazilian Ministry of Science and Technology (the “FINEP Credit Facility”) to finance a research and development project on sugarcane-based biodiesel (see Note 6, "Debt"). The FINEP Credit Facility provides for loans of up to an aggregate principal amount of R$6.4 million (approximately US$2.9 million based on the exchange rate as of September 30, 2013), which was available to the Company in four disbursements and is guaranteed by a chattel mortgage on certain equipment of the Company. The Company's total acquisition cost for the equipment under this guarantee is approximately R$6.0 million (approximately US$2.7 million based on the exchange rate as of September 30, 2013). Through December 31, 2012, the Company received all four disbursements after meeting certain terms and conditions for availability under the FINEP Credit Facility, as described in more detail in Note 6, "Debt." After the release of the first disbursement and prior to any subsequent drawdown from the FINEP Credit Facility, the Company provided bank letters of guarantee of R$3.3 million (approximately US$1.5 million based on the exchange rate as of September 30, 2013) through Banco ABC Brasil S.A. ("ABC Bank"). As of September 30, 2013, all available credit under this facility was fully drawn.

	The Company has a credit facility with Banco Nacional de Desenvolvimento Econômico e Social ("BNDES”), a government-owned bank headquartered in Brazil (the "BNDES Credit Facility") to finance a production site in Brazil. The BNDES Credit Facility provides for loans of up to an aggregate principal amount of R$22.4 million (approximately US$10.0 million based on the exchange rate at September 30, 2013). This credit facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets with a total acquisition cost of R$24.9 million (approximately US$11.2 million based on the exchange rate as of September 30, 2013). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company is required to provide certain bank guarantees under the BNDES Credit Facility.

	The Company entered into loan agreements and a security agreement where the Company pledged certain farnesene production assets as collateral (the fiduciary conveyance of movable goods) with each of Banco Nossa Caixa ("Nossa Caixa") and Banco Pine. Under the loan agreements, Banco Pine agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million as financing for capital expenditures relating to the Company's production facility in Brotas, Brazil. The Company's total acquisition cost for the farnesene production assets pledged as collateral under these agreements is approximately R$68.0 million (approximately US$30.5 million based on the exchange rate as of September 30, 2013). The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements.

	The Company has an export financing agreement for approximately $2.5 million for a one-year term to fund exports through March 2014. This loan is collateralized by future exports from the Company's subsidiary in Brazil.

	Under an operating lease agreement for its office facilities in Brazil, which commenced on November 15, 2011, the Company is required to maintain restricted cash or letters of credit equal to 3 months of rent of approximately R$0.2 million (approximately US$0.1 million based on the exchange rate as of September 30, 2013) in the aggregate as a guarantee that the Company will meet its performance obligations under such operating lease agreement.

	Purchase Obligations

	As of September 30, 2013, the Company had $11.8 million in purchase obligations which included $11.1 million in non-cancellable contractual obligations and construction commitments, of which $4.0 million have been accrued as a loss on purchase commitments.

	On June 25, 2013, the Company and Tate & Lyle Ingredients Americas LLC (“Tate & Lyle”) entered into a Settlement Agreement, Termination Agreement and Mutual Release (the “Termination Agreement”) to terminate the parties’ November 2010 contract manufacturing agreement. Under the Termination Agreement, no further payments will be owed for the remaining term of the Contract Manufacturing Agreement (i.e., through 2016). In the third quarter of 2013, the Company paid $6.2 million of its obligation pertaining to the Termination Agreement. As of September 30, 2013, the Company has an outstanding liability of $2.6 million pertaining to its obligation under the Termination Agreement.

	Other Matters

	Certain conditions may exist as of the date the financial statements are issued which may result in a loss to the Company but will only be recorded when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgment. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

	If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed.

	In May 2013, a securities class action complaint was filed against the Company and its CEO, John G. Melo, in the U.S. District Court for the Northern District of California. In October 2013, the lead plaintiffs filed a consolidated amended complaint. The complaint, as amended, seeks unspecified damages on behalf of a purported class that would comprise all individuals who acquired the Company's common stock between April 29, 2011 and February 8, 2012. The complaint alleges securities law violations based on the Company's commercial projections during that period. The Company believes the complaint lacks merit, and intends to defend itself vigorously. Because the case is at a very early stage and no specific monetary demand has been made, it is not possible for us to estimate the potential loss or range of potential losses for the case.

In August 2013, a complaint entitled Steve Shannon, derivatively on behalf of Amyris, Inc. v. John G. Melo et al and Amyris, Inc., was filed against the Company as nominal defendant in the United States District Court for the Northern District of California. The lawsuit seeks unspecified damages on behalf of the Company from certain of its current and former officers, directors and employees and alleges these defendants breached their fiduciary duties to the Company and unjustly enriched themselves by making allegedly false and misleading statements and omitting certain material facts in our securities filings. Because this purported stockholder derivative action is based on substantially the same facts as the securities class action described above, the two actions have been related and will be heard by the same judge. The Company does not believe the claims in the complaint have merit, and intends to defend itself vigorously. Because the case is at a very early stage and no specific monetary demand has been made, it is not possible to estimate the potential loss or range of potential losses for the case.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with assurance. Therefore, if one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management’s expectations, the Company’s consolidated financial statements for the relevant reporting period could be materially adversely affected.

Debt

Debt	9 Months Ended
	Sep. 30, 2013
Debt Disclosure [Abstract]	'
Debt	'
	Debt

	Debt is comprised of the following (in thousands):



		September 30,				December 31,
		2013				2012
	Credit facilities	$	9,750			$	12,409

	Notes payable	—				1,572

	Convertible notes	25,000				25,000

	Related party convertible notes	58,091				39,033

	Loans payable	25,997				26,150

	Total debt	118,838				104,164

	Less: current portion	(5,448		)		(3,325		)
	Long-term debt	$	113,390			$	100,839


	FINEP Credit Facility

	In November 2010, the Company entered into the FINEP Credit Facility. The FINEP Credit Facility was extended to partially fund expenses related to the Company’s research and development project on sugarcane-based biodiesel (“FINEP Project”) and provided for loans of up to an aggregate principal amount of R$6.4 million (approximately US$2.9 million based on the exchange rate as of September 30, 2013) which is secured by a chattel mortgage on certain equipment of the Company as well as by bank letters of guarantee. All available credit under this facility has been fully drawn.

	Interest on loans drawn under the FINEP Credit Facility is fixed at 5% per annum. In case of default under or non-compliance with the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil (such rate, the “TJLP”). If the TJLP at the time of default is greater than 6%, then the interest will be 5% plus a TJLP adjustment factor, otherwise the interest will be at 11% per annum. In addition, a fine of up to 10% shall apply to the amount of any obligation in default. Interest on late balances will be 1% interest per month, levied on the overdue amount. Payment of the outstanding loan balance is being made in 81 monthly installments, which commenced in July 2012 and extends through March 2019. Interest on loans drawn and other charges are paid on a monthly basis and commenced in March 2011. As of September 30, 2013 and December 31, 2012, the total outstanding loan balance under this credit facility was R$5.5 million (approximately US$2.5 million based on the exchange rate as of September 30, 2013) and R$6.4 million (approximately US$3.1 million based on the exchange rate as of December 31, 2012), respectively.

	The FINEP Credit Facility contains the following significant terms and conditions:

	•	The Company was required to share with FINEP the costs associated with the FINEP Project. At a minimum, the Company was required to contribute from its own funds approximately R$14.5 million (approximately US$6.5 million based on the exchange rate as of September 30, 2013) of which R$11.1 million was to be contributed prior to the release of the second disbursement. All four disbursements were completed and the Company has fulfilled all of its cost sharing obligations;

	•	After the release of the first disbursement, prior to any subsequent drawdown from the FINEP Credit Facility, the Company was required to provide bank letters of guarantee of up to R$3.3 million in aggregate (approximately US$1.5 million based on the exchange rate as of September 30, 2013). On December 17, 2012 and prior to release of the second disbursement on December 26, 2012, the Company obtained the required bank letter of guarantees from ABC Bank;

	•	Amounts disbursed under the FINEP Credit Facility were required to be used by the Company towards the FINEP Project within 30 months after the contract execution.

	BNDES Credit Facility

	In December 2011, the Company entered into the BNDES Credit Facility in the amount of R$22.4 million (approximately US$10.0 million based on the exchange rate at September 30, 2013). This BNDES Credit Facility was extended as project financing for a production site in Brazil. The credit line is divided into an initial tranche for up to approximately R$19.1 million (approximately US$8.6 million based on the exchange rate at September 30, 2013) and an additional tranche of approximately R$3.3 million (approximately US$1.5 million based on the exchange rate at September 30, 2013) to become available upon delivery of additional guarantees. The credit line was available for 12 months from the date of the Credit Facility, subject to extension by the lender.
	The principal of the loans under the BNDES Credit Facility was required to be repaid in 60 monthly installments, with the first installment due in January 2013 and the last due in December 2017. Interest was due initially on a quarterly basis with the first installment due in March 2012. From and after January 2013, interest payments are due on a monthly basis together with principal payments. The loaned amounts carry interest of 7% per annum. Additionally, there is a credit reserve charge of 0.1% on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid.

	The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets totaling R$24.9 million (approximately US$11.2 million based on the exchange rate as of September 30, 2013). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company was required to provide a bank guarantee equal to 10.0% of the total approved amount (R$22.4 million in total debt) available under this Credit Facility. For advances of the second tranche (above R$19.1 million), the Company is required to provide additional bank guarantees equal to 90.0% of each such advance, plus additional Company guarantees equal to at least 130.0% of such advance. The BNDES Credit Facility contains customary events of default, including payment failures, failure to satisfy other obligations under this credit facility or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material judgments, and changes in control of Amyris Brasil. If any event of default occurs, the Lender may terminate its commitments and declare immediately due all borrowings under the facility. As of September 30, 2013 and December 31, 2012, the Company had R$16.2 million (approximately US$7.3 million based on the exchange rate as of September 30, 2013) and R$19.1 million (approximately US$9.3 million based on the exchange rate as of December 31, 2012), respectively, in outstanding advances under the BNDES Credit Facility.

	Notes Payable

	During the period between May 2008 and October 2008, the Company entered into notes payable agreements with the lessor of its headquarters under which it borrowed a total of $3.3 million for the purchase of tenant improvements, bearing an interest rate of 9.5% per annum and to be repaid over a period of 55 to 120 months. As of September 30, 2013 and December 31, 2012, a principal amount of zero and $1.6 million, respectively, was outstanding under these notes payable. In June 2013, as part of the April 30, 2013 Amendment to the Company's operating lease for its headquarters, the Company recorded the elimination of these notes payable as a lease incentive and recorded approximately $1.4 million to deferred rent liability in the condensed consolidated balance sheet. The deferred rent liability is being amortized to expense over the remaining lease term.

	Convertible Notes

	In February 2012, the Company completed the sale of senior unsecured convertible promissory notes in an aggregate principal amount of $25.0 million pursuant to a securities purchase agreement, between the Company and certain investment funds affiliated with Fidelity Investments Institutional Services Company, Inc. (the "Fidelity Securities Purchase Agreement"). The offering consisted of the sale of 3.0% senior unsecured convertible promissory notes with a March 1, 2017 maturity date and an initial conversion price equal to $7.0682 per share of the Company's common stock, subject to proportional adjustment for adjustments to outstanding common stock and anti-dilution provisions in case of dividends and distributions (the "Fidelity Notes"). As of September 30, 2013, the Fidelity Notes were convertible into an aggregate of up to 3,536,968 shares of the Company's common stock. The note holders have a right to require repayment of 101% of the principal amount of the Fidelity Notes in an acquisition of the Company, and the notes provide for payment of unpaid interest on conversion following such an acquisition if the note holders do not require such repayment. The Fidelity Securities Purchase Agreement and Fidelity Notes include covenants regarding payment of interest, maintaining the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The Fidelity Notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, material adverse effect clauses and breaches of the covenants in the Fidelity Securities Purchase Agreement and Fidelity Notes, with default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the Fidelity Notes include restrictions on the amount of debt the Company is permitted to incur. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the Fidelity Notes provide that the Company's total outstanding debt at any time cannot exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125.0 million or 30% of its consolidated total assets. In connection with the Company’s closing of a short-term bridge loan for $35.0 million in October 2013, holders of the Fidelity Notes waived compliance with the debt limitations outlined above as to the $35.0 million bridge loan and the August 2013 Financing. In consideration for such waiver, the Company granted to holders of the Fidelity Notes or their affiliates, the right to purchase up to an aggregate of $7.6 million worth of convertible promissory notes in the first tranche of the August 2013 Financing. As of September 30, 2013 and December 31, 2012, a principal amount of $25.0 million and $25.0 million, respectively, was outstanding under these notes payable.

	Related Party Convertible Notes

	In July 2012, the Company entered into an agreement with Total that expanded Total's investment in Biofene collaboration with the Company, provided a new structure for a joint venture (the “Fuels JV”) to commercialize the products encompassed by the diesel and jet fuel research and development program (the “Program”), and established a convertible debt structure for the collaboration funding from Total.

	The purchase agreement for the notes related to the funding from Total (the "Total Purchase Agreement") provided for the sale of an aggregate of $105.0 million in notes as follows:


	•	As part of an initial closing under the purchase agreement (which initial closing was completed in two installments), (i) on July 30, 2012, the Company sold a 1.5% Senior Unsecured Convertible Note Due March 2017 to Total in the face amount of $38.3 million, including $15.0 million in new funds and $23.3 million in previously-provided diesel research and development funding by Total, and (ii) on September 14, 2012, the Company sold another note (in the same form) for $15.0 million in new funds from Total.

	•	At a second closing under the Total Purchase Agreement (also completed in two installments) the Company sold additional notes for an aggregate of $30 million in new funds from Total ($10.0 million in June 2013 and $20.0 million in July 2013).

•	The Total Purchase Agreement provides that additional notes may be sold in subsequent closings in July 2014 (for cash proceeds to the Company of $21.7 million, which would be settled in an initial installment of $10.85 million payable at such closing and a second installment of $10.85 million payable in January 2015).

The notes issued have a maturity date of March 1, 2017, an initial conversion price equal to $7.0682 per share for the notes issued under the initial closing and an initial conversion price equal $3.08 per share for the notes issued under the second closing. The notes bear interest of 1.5% per annum (with a default rate of 2.5%), accruing from the date of funding and are payable at maturity or on conversion or a change of control where Total exercises the right to require the Company to repay the notes. Accrued interest is cancelled if the notes are cancelled based on a “Go” decision. The agreements contemplate that the research and development efforts under the Program may extend through 2016, with a series of “Go/No Go” decisions by Total through such date tied to funding by Total.

The notes become convertible into the Company's common stock (i) within 10 trading days prior to maturity (if they are not cancelled as described above prior to their maturity date), (ii) on a change of control of the Company, (iii) if Total is no longer the largest stockholder of the Company following a “No-Go” decision (subject to a six-month lock-up with respect to any shares of common stock issued upon conversion), and (iv) on a default by the Company. If Total makes a final “Go” decision, then the notes will be exchanged by Total for equity interests in the Fuels JV, after which the notes will not be convertible and any obligation to pay principal or interest on the notes will be extinguished. If Total makes a “No-Go” decision, outstanding notes will remain outstanding and become payable at maturity.

In connection with the December 2012 private placement described below (see Note 10, "Stockholders Equity"), Total elected to participate in the private placement by exchanging approximately $5.0 million of its $53.3 million in senior unsecured convertible promissory notes then outstanding for 1,677,852 of the Company's common stock at a conversion price of $2.98 per share. As such, $5.0 million of the outstanding $53.3 million in senior unsecured convertible promissory notes was cancelled. The cancellation of the debt was treated as an extinguishment of debt in accordance with the guidance outlined in ASC 470-50.

In March 2013, the Company entered into a letter agreement with Total (the "March 2013 Letter Agreement") under which Total agreed to waive its right to cease its participation in the parties' fuels collaboration at the July 2013 decision point and committed to proceed with the July 2013 funding tranche of $30.0 million (subject to the Company's satisfaction of the relevant closing conditions for such funding in the Total Purchase Agreement). As consideration for this waiver and commitment, the Company agreed to:

•	Reduce the conversion price for the senior unsecured convertible promissory notes to be issued in connection with such funding from $7.0682 per share to a price per share equal to the greater of (i) the consolidated closing bid price of the Company's common stock on the date of the letter agreement, plus $0.01, and (ii) $3.08 per share, provided that the conversion price would not be reduced by more than the maximum possible amount permitted under the rules of NASDAQ Stock Market ("NASDAQ") such that the new conversion price would require the Company to obtain stockholder consent; and

•	Grant Total a senior security interest in the Company's intellectual property, subject to certain exclusions and subject to release by Total when the Company and Total enter into final documentation regarding the establishment of the Fuels JV.

In addition to the waiver by Total described above, Total also agreed that, at the Company's request and contingent upon the Company meeting its obligations described above, it would pay advance installments of the amounts otherwise payable at the July 2013 closing. Specifically, if the Company requested such advance installments, subject to certain closing conditions and delivery of certifications regarding the Company's cash levels, Total was obligated to fund $10.0 million no later than May 15, 2013, and an additional $10.0 million no later than June 15, 2013, with the remainder to be funded on the original July 2013 closing date.

In June 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $10.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above. In accordance with the March 2013 Letter Agreement, this convertible note has an initial conversion price equal to $3.08 per share of the Company's common stock. The Company did not request the May advance of $10.0 million, but did request the June advance (as described above), under which this convertible note was issued.

In July 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $20.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above. This purchase and sale completed Total's commitment to purchase $30.0 million of such notes by July 2013. In accordance with the March 2013 Letter Agreement, this convertible note has an initial conversion price equal to $3.08 per share of Company common stock.

The conversion prices of the notes issued under the Total Purchase Agreement are subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. Total has a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if Total does not require such repayment. The Total Purchase Agreement and notes include covenants regarding payment of interest, maintenance of the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the purchase agreement and notes, with added default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the notes include restrictions on the amount of debt the Company is permitted to incur. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the notes provide that the Company's total outstanding debt at any time cannot exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125.0 million or 30% of its consolidated total assets. In connection with the Company’s closing of a short-term bridge loan for $35.0 million in October 2013, Total waived compliance with the debt limitations outlined above as to the $35.0 million bridge loan and the August 2013 Financing. As of September 30, 2013 and December 31, 2012, $58.1 million and $39.0 million, respectively, was outstanding under these convertible notes, net of debt discount of $20.2 million and $9.3 million, respectively. The debt discount is the result of the bifurcation of the equity conversion option and "make-whole" provision features associated with outstanding debt.

In connection with the August 2013 Financing, the Company entered into a Securities Purchase Agreement ("August 2013 SPA") with Total and Temasek to sell up to $73.0 million in convertible promissory notes in private placements, with such notes to be sold and issued over a period of up to 24 months from the date of signing. The August 2013 SPA provided for the August 2013 Financing to be divided into two tranches (the first tranche for $42.6 million and the second tranche for $30.4 million), each with differing closing conditions. Of the total possible purchase price in the financing, $60.0 million was contemplated to be paid in the form of cash by Temasek ($35.0 million in the first tranche and up to $25.0 million in the second tranche) and $13.0 million was contemplated to be paid by the exchange and cancellation of outstanding convertible promissory notes by Total in connection with its exercise of pro rata rights ($7.6 million in the first tranche and $5.4 million in the second tranche). The August 2013 SPA included requirements that the Company meet certain production milestones before the second tranche would become available, obtain stockholder approval prior to completing any closing of the transaction, and issue a warrant to Temasek to purchase 1,000,000 shares of the Company's common stock at an exercise price of $0.01 per share, exercisable only if Total converts preexisting promissory notes with a certain per share conversion price. In September 2013, the Company's stockholders approved the August 2013 Financing. As of September 30, 2013, the first closing of the August 2013 Financing was pending final regulatory approval.

In October 2013, the Company amended the August 2013 SPA to include an additional cash investor in the first tranche convertible promissory notes in the principal amount of $7.6 million, and to proportionally increase the amount acquired by exchange and cancellation of outstanding convertible promissory notes by Total in connection with its exercise of pro rata rights to $14.6 million (US$9.2 million in the first tranche and up to $5.4 million in the second tranche). The August 2013 Financing closed with respect to the initial tranche of notes in October 2013 (see Note 17, "Subsequent Events"). Additional closing conditions for the second tranche of up to $30.4 million in principal amount of additional convertible promissory notes, which may be issued up to 24 months from the date of the August 2013 SPA, include requirements that prior to any issuance of such notes: (i) a specified Company manufacturing plant has achieved total production of 750,000 liters within a run period of 45 days, (ii) the current chief executive officer or an individual approved by a majority of the purchasers remains chief executive officer of the Company, (iii) there is no material adverse change in the Company’s business and (iv) all security interests held by the purchasers in the Company’s intellectual property shall have been released in full.

In September 2013, the Company entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million. As of September 30, 2013, the Company had not drawn any funds from the agreement and the facility expired in October 2013 in accordance with its terms.

Loans Payable

In December 2009, the Company entered into a loans payable agreement with the lessor of its Emeryville pilot plant under which it borrowed a total of $0.3 million, bearing an interest rate of 10.0% per annum, to be repaid over a period of 96 months. As of September 30, 2013 and December 31, 2012, a principal amount of zero and $0.2 million, respectively, was outstanding under the loan. During the three months ended June 30, 2013, as part of the April 30, 2013 amendment entered into regarding the Company's operating lease for its headquarters, the Company recorded the elimination of this loan payable as a lease incentive and recorded approximately $0.2 million to deferred rent liability in the condensed consolidated balance sheet. The deferred rent liability is being amortized to expense over the remaining lease term.

In June 2012, the Company entered into a loan agreement with Banco Pine under which Banco Pine provided the Company with the Banco Pine Bridge Loan of R$52.0 million (approximately US$25.6 million based on the exchange rate as of September 30, 2012, the time of loan repayment). The interest rate for the Banco Pine Bridge Loan was 0.4472% monthly (approximately 5.5% on an annualized basis). The principal and interest due under the Banco Pine Bridge Loan matured and were required to be repaid on September 19, 2012, subject to extension by Banco Pine. At the time of the Banco Pine Bridge Loan, the Company entered into a currency interest rate swap arrangement with the lender for R$22.0 million (approximately US$9.9 million based on the exchange rate as of September 30, 2013). The interest rate swap arrangement exchanged the principal and interest payments under the Banco Pine Loan of R$22.0 million entered into in July 2012 for alternative principal and interest payments that were subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap had a fixed interest rate of 3.94%. In July 2012, the Company repaid the Banco Pine Bridge Loan.

In July 2012, the Company entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods Agreement (together, the "July 2012 Bank Agreements") with each of Nossa Caixa and Banco Pine. Under the July 2012 Bank Agreements, the Company pledged certain farnesene production assets as collateral for the loans of R$52.0 million. The Company's total acquisition cost for such pledged assets was approximately R$68.0 million (approximately US$30.5 million based on the exchange rate as of September 30, 2013). The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. Under the July 2012 Bank Agreements, the Company could borrow an aggregate of R$52.0 million (approximately US$23.3 million based on the exchange rate as of September 30, 2013) as financing for capital expenditures relating to the Company's manufacturing facility located in Brotas, Brazil. Specifically, Banco Pine agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million. The funds for the loans are provided by BNDES, but are guaranteed by the lenders. The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year. The loans are also subject to early maturity and delinquency charges upon occurrence of certain events including interruption of manufacturing activities at the Company's manufacturing facility in Brotas, Brazil for more than 30 days, except during sugarcane off-season. For the first two years that the loans are outstanding, the Company is required to pay interest only on a quarterly basis. After August 15, 2014, the Company is required to pay equal monthly installments of both principal and interest for the remainder of the term of the loans. As of September 30, 2013 and December 31, 2012, a principal amount of $23.3 million and $25.4 million, respectively, was outstanding under these loan agreements.

In October 2012, the Company entered into a loan payable agreement with a lender under which it borrowed $0.6 million to pay the insurance premiums of certain policies. The loan was payable in nine monthly installments of principal and interest. Interest accrued at a rate of 3.24% per annum. As of September 30, 2013 and December 31, 2012, the outstanding unpaid loan balance was zero and $0.4 million, respectively.

In March 2013, the Company entered into an export financing agreement with ABC Bank for approximately $2.5 million for a one-year term to fund exports through March 2014. This loan is collateralized by future exports from the Company's subsidiary in Brazil. As of September 30, 2013, the principal amount outstanding under this agreement was $2.5 million.

Letters of Credit

In June 2012, the Company entered into a letter of credit agreement for $1.0 million under which it provided a letter of credit to the landlord for its headquarters in Emeryville, California in order to cover the security deposit on the lease. This letter of credit is secured by a certificate of deposit. Accordingly, the Company has $1.0 million as restricted cash as of September 30, 2013 and December 31, 2012.

Future minimum payments under the debt agreements as of September 30, 2013 are as follows (in thousands):



Years ending December 31:	Related Party Convertible Debt				Convertible Debt				Loans Payable			Credit Facility
2013 (Remaining three months)	$	—			$	192			$	492		$	682

2014	—				760				5,243			2,681

2015	—				765				4,042			2,542

2016	—				761				3,887			2,404

2017	83,267				25,125				3,726			2,264

Thereafter	—				—				15,052			579

Total future minimum payments	83,267				27,603				32,442			11,152

Less: amount representing interest(1)	(25,176		)		(2,603		)		(6,445		)	(1,402		)
Present value of minimum debt payments	58,091				25,000				25,997			9,750

Less: current portion	—				—				(3,286		)	(2,162		)

Noncurrent portion of debt	$	58,091			$	25,000			$	22,711		$	7,588

Joint_Ventures_and_Noncontroll

Joint Ventures and Noncontrolling Interest	9 Months Ended
	Sep. 30, 2013
Joint Ventures and Noncontrolling Interest [Abstract]	'
Joint Ventures and Noncontrolling Interest	'
	Joint Ventures and Noncontrolling Interest

	SMA Indústria Química

	In April 2010, the Company established SMA Indústria Química ("SMA"), a joint venture with Usina São Martinho, to build a production facility in Brazil. SMA is located at the Usina São Martinho mill in Pradópolis, São Paulo state. The joint venture agreements establishing SMA have a 20 year initial term.

	SMA is managed by a three member executive committee, of which the Company appoints two members, one of whom is the plant manager, who is the most senior executive responsible for managing the construction and operation of the facility. SMA is governed by a four member board of directors, of which the Company and Usina São Martinho each appoint two members. The board of directors has certain protective rights which include final approval of the engineering designs and project work plan developed and recommended by the executive committee.

	The joint venture agreements provided that the Company would fund the construction costs of the new facility and Usina São Martinho would reimburse the Company up to R$61.8 million (approximately $27.7 million based on the exchange rate as of September 30, 2013) of the construction costs after SMA commences production. After commercialization, the Company would market and distribute Company renewable products produced by SMA and Usina São Martinho would sell feedstock and provide certain other services to SMA. The cost of the feedstock to SMA would be a price that is based on the average return that Usina São Martinho could receive from the production of its current products, sugar and ethanol. The Company would be required to purchase the output of SMA for the first four years at a price that guarantees the return of Usina São Martinho’s investment plus a fixed interest rate. After this four year period, the price would be set to guarantee a break-even price to SMA plus an agreed upon return.

	Under the terms of the joint venture agreements, if the Company becomes controlled, directly or indirectly, by a competitor of Usina São Martinho, then Usina São Martinho has the right to acquire the Company’s interest in SMA. If Usina São Martinho becomes controlled, directly or indirectly, by a competitor of the Company, then the Company has the right to sell its interest in SMA to Usina São Martinho. In either case, the purchase price shall be determined in accordance with the joint venture agreements, and the Company would continue to have the obligation to acquire products produced by SMA for the remainder of the term of the supply agreement then in effect even though the Company would no longer be involved in SMA’s management.

	The Company has a 50% ownership interest in SMA. The Company has identified SMA as a variable interest entity ("VIE") pursuant to the accounting guidance for consolidating VIEs because the amount of total equity investment at risk is not sufficient to permit SMA to finance its activities without additional subordinated financial support, as well as because the related commercialization agreement provides a substantive minimum price guarantee. Under the terms of the joint venture agreement, the Company directs the design and construction activities, as well as production and distribution. In addition, the Company has the obligation to fund the design and construction activities until commercialization is achieved. Subsequent to the construction phase, both parties equally fund SMA for the term of the joint venture. Based on those factors, the Company was determined to have the power to direct the activities that most significantly impact SMA’s economic performance and the obligation to absorb losses and the right to receive benefits. Accordingly, the financial results of SMA are included in the Company’s condensed consolidated financial statements and amounts pertaining to Usina São Martinho’s interest in SMA are reported as noncontrolling interests in subsidiaries.

	Novvi S.A.

	In June 2011, the Company entered into joint venture agreements with Cosan Combustíveis e Lubrificantes S.A. and Cosan S.A. Industria e Comércio (such Cosan entities, collectively or individually, “Cosan”), related to the formation of a joint venture to focus on the worldwide development, production and commercialization of base oils made from Biofene for the automotive, commercial and industrial lubricants markets (the "Original JV Agreement"). The parties originally envisioned operating their joint venture through Novvi S.A., a Brazilian entity jointly owned by Cosan and Amyris Brasil.

	Under the Original JV Agreement and related agreements, the Company and Cosan each owned 50% of Novvi S.A. and each party would share equally any costs and any profits ultimately realized by Novvi S.A. The joint venture agreement had an initial term of 20 years from the date of the Original JV Agreement, subject to earlier termination by mutual written consent or by a non-defaulting party in the event of specified defaults by the other party. The shareholders' agreement had an initial term of 10 years from the date of the agreement, subject to earlier termination if either the Company or Cosan ceased to own at least 10% of the voting stock of Novvi S.A. Since its formation, Novvi S.A. had minimal operating activities while the Company and Cosan continued to determine and finalize the strategy and operating activities for the joint venture. Upon determination by the Company and Cosan that the joint venture should be operated out of a US entity, the operating activities of Novvi S.A. ceased. The Company has identified that Novvi S.A. is a VIE and determined that the power to direct activities, which most significantly impact the economic success of the joint venture, is equally shared between the Company and Cosan. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in Novvi S.A. under the equity method of accounting.

	In March 2013, the Company, Amyris Brasil and Cosan entered into a termination agreement to terminate the Original JV Agreement. In addition, Amyris Brasil agreed to sell, its 50% ownership in Novvi S.A. for approximately R$22,000 which represented the current value of its 50% equity ownership in Novvi S.A., a now-dormant company, to Cosan. Upon the consummation of the transaction with the shares transferring from Amyris Brasil to Cosan, the Novvi S.A. shareholders agreement automatically terminated.

	Novvi LLC

	In September 2011, the Company and Cosan US, Inc. (“Cosan U.S.”) formed Novvi LLC, a U.S. entity that is jointly owned by the Company and Cosan U.S. ("Novvi"). In March 2013 the Company and Cosan U.S. entered into agreements to (i) expand their base oils joint venture to also include additives and lubricants and (ii) operate their joint venture exclusively through Novvi. Specifically, the parties entered into an Amended and Restated Operating Agreement for Novvi (the "Operating Agreement"), which sets forth the governance procedures for Novvi and the joint venture and the parties' initial contribution. The Company also entered into an IP License Agreement with Novvi (the "IP License Agreement") under which the Company granted Novvi (i) an exclusive (subject to certain limited exceptions for the Company), worldwide, royalty-free license to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in automotive and industrial lubricants markets and (ii) a non-exclusive, royalty free license, subject to certain conditions, to manufacture Biofene solely for its own products. In addition, both the Company and Cosan U.S. granted Novvi certain rights of first refusal with respect to alternative base oil and additive technologies that may be acquired by the Company or Cosan U.S. during the term of the IP License Agreement. Under these agreements, the Company and Cosan U.S. will each own 50% of Novvi and each party will share equally in any costs and any profits ultimately realized by the joint venture. Novvi is governed by a six member Board of Managers (the "Board Managers"), with three managers represented by each investor. The Board of Managers appoints the officers of Novvi, who are responsible for carrying out the daily operating activities of Novvi as directed by the Board of Managers. The IP License Agreement has an initial term of 20 years from the date of the agreement, subject to standard early termination provisions such as uncured material breach or a party's insolvency. Under the terms of the Operating Agreement, Cosan U.S. is obligated to fund its 50% ownership share of Novvi in cash in the amount of $10.0 million and the Company is obligated to fund its 50% ownership share of Novvi through the granting of an IP License to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in the automotive, commercial and industrial lubricants markets which has been agreed upon by Cosan U.S. and Amyris valued at $10.0 million. In March 2013, the Company measured its initial contribution of intellectual property to Novvi at the Company's carrying value of the licenses granted under the IP License Agreement, which was zero. Additional funding requirements to finance the ongoing operations of Novvi are expected to happen through revolving credit or other loan facilities provided by unrelated parties (i.e. such as financial institutions); cash advances or other credit or loan facilities provided by the Company and Cosan U.S. or their affiliates; or additional capital contributions by the Company and Cosan U.S.

	The Company has identified Novvi as a VIE and determined that the power to direct activities, which most significantly impact the economic success of the joint venture (i.e. continuing research and development, marketing, sales, distribution and manufacturing of Novvi products), is equally shared between the Company and Cosan U.S. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in Novvi under the equity method of accounting. The Company will continue to reassess its primary beneficiary analysis of Novvi if there are changes in events and circumstances impacting the power to direct activities that most significantly affect Novvi's economic success. Under the equity method, the Company's share of profits and losses are included in “Income (loss) from equity method investments, net” in the condensed consolidated statements of operations. During the three and nine months ended September 30, 2013, the Company recorded no amounts for its share of Novvi's net loss as the carrying amount of the Company's investment in Novvi was zero and losses in excess of the carrying amount were offset by the accretion of the Company's share in the basis difference resulting from the parties' initial contribution. For both the three months ended September 30, 2013 and 2012, the Company recorded zero and for the nine months ended September 30, 2013 and 2012, the Company recorded $2.6 million and zero, respectively, of revenue from the research and development activities that it has performed on behalf of Novvi. In addition, for the three and nine months ended September 30, 2013, we recognized $1.0 million and $1.1 million in product sales, respectively, from Novvi.

	Glycotech

	In January 2011, the Company entered into a production service agreement ("Glycotech Agreement") with Glycotech, Inc. ("Glycotech"), under which Glycotech provides process development and production services for the manufacturing of various Company products at its leased facility in Leland, North Carolina. The Company products manufactured by Glycotech are owned and distributed by the Company. Pursuant to the terms of the production Glycotech Agreement, the Company is required to pay the manufacturing and operating costs of the Glycotech facility, which is dedicated solely to the manufacture of Amyris products. The initial term of the Glycotech Agreement was for a two-year period commencing on February 1, 2011 and the Glycotech Agreement renews automatically for successive one-year terms, unless terminated by the Company. Concurrently with the Glycotech Agreement, the Company also entered into a Right of First Refusal Agreement with the lessor of the facility and site leased by Glycotech (the "ROFR Agreement"). Per the conditions of the ROFR Agreement, the lessor agreed not to sell the facility and site leased by Glycotech during the term of the Glycotech Agreement. In the event that the lessor is presented with an offer to sell or decides to sell an adjacent parcel, the Company has the right of first refusal to acquire it.

	The Company has determined that the arrangement with Glycotech qualifies as a VIE. The Company determined that it is the primary beneficiary of this arrangement because it has the power through the management committee over which it has majority control to direct the activities that most significantly impact Glycotech's economic performance. In addition, the Company is required to fund 100% of Glycotech's actual operating costs for providing services each month while the facility is in operation under the Glycotech Agreement. Accordingly, the Company consolidates the financial results of Glycotech. As of September 30, 2013, the carrying amounts of the consolidated VIE's assets and liabilities were not material to the Company's condensed consolidated financial statements.

	The table below reflects the carrying amount of the assets and liabilities of the two consolidated VIEs for which the Company is the primary beneficiary. As of September 30, 2013, the assets include $22.7 million in property, plant and equipment, $4.1 million in other assets and $0.4 million in current assets. The liabilities include $0.2 million in accounts payable and accrued current liabilities and $0.1 million in loan obligations by Glycotech to its shareholders that are non-recourse to the Company. The creditors of each consolidated VIE have recourse only to the assets of that VIE.




		September 30,			December 31,
	(In thousands)	2013			2012
	Assets	$	27,118		$	29,564

	Liabilities	$	335		$	355

	The change in noncontrolling interest for the nine months ended September 30, 2013 and 2012 is summarized below (in thousands):


		2013			2012
	Balance at January 1	$	(877	)	$	(240	)
	Foreign currency translation adjustment	55			209

	Gain (loss) attributable to noncontrolling interest	232			(772		)

	Balance at September 30	$	(590	)	$	(803	)

Significant_Agreements

Significant Agreements	9 Months Ended
Significant Agreements	Sep. 30, 2013
Significant Agreements [Abstract]	'
Significant Agreements	'
	Significant Agreements

	Tate & Lyle Termination Agreement

	In June 2013, the Company and Tate & Lyle entered into a Termination Agreement to terminate the parties’ November 2010 contract manufacturing agreement (the “Contract Manufacturing Agreement”). The Termination Agreement resolves all outstanding issues that had arisen in connection with the Company’s relationship with Tate & Lyle.

	The Contract Manufacturing Agreement had secured manufacturing capacity for farnesene through 2016 at Tate & Lyle’s facility in Decatur, Illinois. The Contract Manufacturing Agreement included a base monthly payment and a variable payment based on production volume at the Tate & Lyle facility. With the Company’s commencement of production at its farnesene facility located in Brazil, the Company determined that the Contract Manufacturing Agreement was no longer desired from a cost and operational perspective. The Company had no production at the Tate & Lyle facility since the first quarter of 2013.

	Pursuant to the Termination Agreement, the Company is required to make four payments to Tate & Lyle, totaling approximately $8.8 million, of which $3.6 million is to satisfy outstanding obligations and $5.2 million is in lieu of additional payments otherwise owed under the Contract Manufacturing Agreement. These four payments are due under the Termination Agreement between July 17, 2013 and December 16, 2013, and are deemed to be in full satisfaction of all amounts otherwise owed under the Contract Manufacturing Agreement. Under the Termination Agreement, no further payments will be owed for the remaining term of the Contract Manufacturing Agreement (i.e., through 2016). As a result, the Company recorded a loss of $8.4 million which is included in the loss on purchase commitments and write-off of production assets and consisted of an impairment charge of $6.7 million relating to Company-owned equipment at the Tate & Lyle facility, a $2.7 million write off of an unamortized portion of equipment costs funded by the Company for Tate & Lyle, offset by a reversal of $1.0 million provision for loss on fixed purchase commitments. As of September 30, 2013. the Company had an outstanding liability of $2.6 million pertaining to its obligations under the Termination Agreement.

	Collaboration Partner Joint Development and License Agreement

	In April 2013, the Company entered into a joint development and license agreement with a collaboration partner. Under the terms of the multi-year agreement, the collaboration partner and the Company will jointly develop certain fragrance ingredients. The collaboration partner will have exclusive rights to these fragrance ingredients for applications in the flavors and fragrances field, and the Company will have exclusive rights in other fields. The collaboration partner and the Company will share in the economic value derived from these ingredients. The joint development and license agreement provides for up to $6.0 million in funding based upon the achievement of certain technical milestones which are considered substantive by the Company during the first phase of the collaboration.

	Collaboration Partner Master Collaboration Agreement

	In March 2013, the Company entered into a Master Collaboration Agreement with a collaboration partner to establish a collaboration for the development and commercialization of multiple renewable flavors and fragrances ("F&F") compounds. Under this agreement, except for rights granted under preexisting collaboration relationships, the Company granted the collaboration partner exclusive access for such compounds to specified Company intellectual property for the development and commercialization of F&F products in exchange for research and development funding and a profit sharing arrangement. The agreement superseded and expanded a prior collaboration agreement between the Company and the collaboration partner.

	The agreement provides annual up-front funding to the Company by the collaboration partner of $10.0 million for each of the first three years of the collaboration. The initial payment of $10.0 million was received by the Company in March 2013 of which $2.5 million and $5.4 million were recognized as revenue for the three and nine months ended September 30, 2013, respectively. The agreement contemplates additional funding by the collaboration partner of up to $5.0 million under three potential milestone payments, as well as additional funding by the collaboration partner on a discretionary basis. Under the Company's revenue recognition policy for milestone payments, for arrangements that include milestones that are determined to be substantive and at risk at the inception of the arrangement, revenue is recognized upon achievement of the milestone and is limited to those amounts whereby collectability is reasonably assured.

	In addition, the agreement contemplates that the parties will mutually agree on a supply price for each compound and share product margins from sales of each compound on a 70/30 basis (70% for the collaboration partner) until the collaboration partner receives $15.0 million more than the Company in the aggregate, after which the parties will share 50/50 in the product margins on all compounds. The Company also agreed to pay a one-time success bonus of up to $2.5 million to the collaboration partner for outperforming certain commercialization targets. The collaboration partner eligibility to receive the one-time success bonus commences upon the first sale of the first the collaboration partner's product.

	The agreement does not impose any specific research and development commitments on either party after year six, but if the parties mutually agree to perform development after year six, the agreement provides that the parties will fund it equally.

	Under the agreement, the parties jointly select target compounds, subject to final approval of compound specifications by the collaboration partner. During the development phase, the Company is required to provide labor, intellectual property and technology infrastructure and the collaboration partner is required to contribute downstream polishing expertise and market access. The agreement provides that the Company will own research and development and strain engineering intellectual property, and the collaboration partner will own blending and, if applicable, chemical conversion intellectual property. Under certain circumstances such as the Company's insolvency, the collaboration partner gains expanded access to the Company's intellectual property. Following development of F&F compounds under the agreement, the agreement contemplates that the Company will manufacture the initial target molecules for the compounds and the collaboration partner will perform any required downstream polishing, distribution, sales and marketing.

Goodwill_and_Intangible_Assets

Goodwill and Intangible Assets (Notes)	9 Months Ended
	Sep. 30, 2013
Goodwill and Intangible Assets Disclosure [Abstract]	'
Goodwill and Intangible Assets	'
	Goodwill and Intangible Assets

	The following table presents the components of the Company's intangible assets (in thousands):



				30-Sep-13								31-Dec-12
		Useful Life in Years		Gross Carrying Amount		Accumulated Amortization			Net Carrying Value			Gross Carrying Amount			Accumulated Amortization			Net Carrying Value
	In-process research and development	Indefinite		$	8,560	$	—		$	8,560		$	8,560		$	—		$	8,560

	Acquired licenses and permits	2		772		(772		)	—			772			(740		)	32

	Goodwill	Indefinite		560		—			560			560						560

				$	9,892	$	(772	)	$	9,120		$	9,892		$	(740	)	$	9,152


	The following table presents the activity of intangible assets for the nine months ended September 30, 2013 (in thousands):



			31-Dec-12														30-Sep-13
			Net Carrying Value			Additions				Adjustments			Amortization				Net Carrying Value
	In-process research and development		$	8,560		$	—			$	—		$	—			$	8,560

	Acquired licenses and permits		32			—				—			(32		)		—

	Goodwill		560			—				—			—				560

			$	9,152		$	—			$	—		$	(32	)		$	9,120


	The intangible assets acquired through the Draths Corporation acquisition in October 2011 of in process research and development of $8.6 million and goodwill of $0.6 million are treated as indefinite lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written-off, as appropriate. If the carrying amount of the assets is greater than the measures of fair value, impairment is considered to have occurred and a write-down of the asset is recorded. Any finding that the value of its intangible assets has been impaired would require the Company to write-down the impaired portion, which could reduce the value of its assets and reduce (increase) its net income (loss) for the year in which the related impairment charges occur. As of September 30, 2013 and December 31, 2012 no impairment on the goodwill and intangible assets were recorded.

	Acquired licenses and permits are amortized using a straight-line method over its estimated useful life. Amortization expense for this intangible was zero and $0.1 million for the three months ended September 30, 2013 and 2012, respectively and was $32,000 and $0.3 million for the nine months ended September 30, 2013 and 2012, respectively. As of September 30, 2013, acquired licenses and permits were fully amortized.

Stockholders_Equity

Stockholders' Equity	9 Months Ended
Stockholders' Equity	Sep. 30, 2013
Stockholders' Equity Note [Abstract]	'
Stockholders' Equity	'
	Stockholders’ Equity

	February 2012 Private Placement

	In February 2012, the Company completed a private placement of 10,160,325 shares of its common stock at a price of $5.78 per share for aggregate proceeds of $58.7 million. In connection with this private placement, the Company entered into an agreement with an investor to purchase additional shares of the Company's common stock for an additional $15.0 million by March 2013 upon satisfaction by the Company of criteria associated with the commissioning of the Company's production plant in Brotas, Brazil. This additional investment was provided by the investor through a $10.0 million investment in a private placement completed by the Company in December 2012 and subsequently, through a $5.0 million investment in a private placement completed by the Company in March 2013.

	May 2012 Private Placement

	In May 2012, the Company completed a private placement of 1,736,100 shares of its common stock at a price of $2.36 per share for aggregate proceeds of $4.1 million.

	December 2012 Private Placement

	In December 2012, the Company completed a private placement of 14,177,849 shares of its common stock at a price of $2.98 per share for aggregate proceeds of $37.2 million and the cancellation of $5.0 million worth of outstanding senior unsecured convertible promissory notes previously issued to Total by the Company. The Company issued 1,677,852 shares to Total in exchange for this note cancellation. Net cash received for this private placement as of December 31, 2012 was $22.2 million and the remaining $15.0 million of proceeds was received in January 2013. In connection with this transaction, the Company entered into a letter agreement with an investor under which the Company acknowledged that the investor's initial investment of $10.0 million in December 2012 represented partial satisfaction of the investor's preexisting contractual obligation to fund $15.0 million by March 31, 2013 upon satisfaction by the Company of criteria associated with the commissioning of the Company's production plant in Brotas, Brazil.

	In January 2013, the Company received $15.0 million in proceeds from the private placement offering that closed in December 2012. Consequently, the Company issued 5,033,557 shares of the 14,177,849 shares of the Company's common stock.

	March 2013 Private Placement

	In March 2013, the Company completed a private placement of 1,533,742 shares of its common stock at a price of $3.26 per share for aggregate proceeds of $5.0 million. This private placement represented the final tranche of an investor's preexisting contractual obligation to fund $15.0 million upon satisfaction by the Company of certain criteria associated with the commissioning of the Company's production plant in Brotas, Brazil.

	Evergreen Shares for 2010 Equity Plan and 2010 ESPP

	On January 23, 2013, the Company's Board of Directors (the "Board") approved an increase to the number of shares available for issuance under the Company's 2010 Equity Incentive Plan (the "Equity Plan") and the 2010 Employee Stock Purchase Plan (the "ESPP"). These shares represent an automatic annual increase in the number of shares available for issuance under the Equity Plan and the ESPP of 3,435,483 and 687,096, respectively, equal to 5% and 1%, respectively, of 68,709,660 shares, the total outstanding shares of the Company’s common stock as of December 31, 2012. This automatic increase was effective as of January 1, 2013. Shares available for issuance under the Equity Plan and ESPP were initially registered on a registration statement on Form S-8 filed with the Securities and Exchange Commission on October 1, 2010 (Registration No. 333-169715). The Company filed registration statements on Form S-8 on March 28, 2013 and May 20, 2013 with respect to the shares added by the automatic increase on January 1, 2013.

StockBased_Compensation_Plans

Stock-Based Compensation Plans	9 Months Ended
	Sep. 30, 2013
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Stock-Based Compensation Plans	'
	Stock-Based Compensation

	The Company’s stock option activity and related information for the nine months ended September 30, 2013 was as follows:



				Number			Weighted Average				Weighted	Aggregate
				Outstanding			Exercise				Average	Intrinsic
							Price				Remaining	Value
											Contractual
											Life (Years)
												(in thousands)
	Outstanding - December 31, 2012			8,946,592			$	9.07			7.5	$	954

		Options granted		2,772,130			$	2.83

		Options exercised		(193,166	)		$	0.87

		Options cancelled		(2,389,042	)		$	9.56

	Outstanding - September 30, 2013			9,136,514			$	7.23			7.72	$	71


	Vested and expected to vest after September 30, 2013			8,454,008			$	7.44			7.61	$	71

	Exercisable at September 30, 2013			3,950,398			$	9.7			6.18	$	71


	The aggregate intrinsic value of options exercised under all option plans was $0.1 million and $2.0 million for the three months ended September 30, 2013 and 2012, respectively, and was $0.4 million and $2.7 million for the nine months ended September 30, 2013 and 2012, respectively, determined as of the date of option exercise.

	The Company’s restricted stock units ("RSUs") and restricted stock activity and related information for the nine months ended September 30, 2013 was as follows:



			RSUs			Weighted Average Grant-Date Fair Value				Weighted Average Remaining Contractual Life (Years)
	Outstanding - December 31, 2012		2,550,799			$	7.92			1.3

		Awarded	1,100,000			$	2.84			—

		Vested	(654,619	)		$	5.91			—

		Forfeited	(360,995	)		$	3.92			—

	Outstanding - September 30, 2013		2,635,185			$	4.2			1.05

	Expected to vest after September 30, 2013		2,389,722			$	4.2			0.98

	The following table summarizes information about stock options outstanding as of September 30, 2013:




		Options Outstanding									Options Exercisable
	Exercise Price	Number of Options			Weighted Average		Weighted Average Exercise Price				Number of Options		Weighted Average Exercise Price
					Remaining Contractual Life
					(Years)
	$0.10—$2.76	1,218,972			8.34		$	2.63			248,047		$	2.31

	$2.79—$2.85	964,895			9.75		$	2.79			68		$	2.85

	$2.87—$2.87	917,000			9.67		$	2.87			—		$	—

	$2.89—$3.12	918,271			9.14		$	2.99			204,297		$	3.04

$3.23—$3.83	189,639			8.79		$	3.31			86,438		$	3.39

$3.86—$3.86	1,045,052			8.16		$	3.86			416,769		$	3.86

$3.93—$4.06	992,731			4.25		$	3.95			926,064		$	3.94

$4.31—$14.28	919,609			6.11		$	6.8			748,254		$	6.38

$16.00—$19.61	942,063			7.05		$	16.31			600,610		$	16.29

$20.41—$30.17	1,028,282			6.84		$	23.86			719,851		$	23.62

$0.10—$30.17	9,136,514			7.72		$	7.23			3,950,398		$	9.7


Stock-Based Compensation Expense

Stock-based compensation expense related to options and restricted stock units granted to employees and nonemployees was allocated to research and development expense and sales, general and administrative expense as follows (in thousands):



	Three Months Ended September 30,								Nine Months Ended September 30,
	2013				2012				2013			2012
Research and development	$	1,132			$	1,450			$	3,428		$	4,521

Sales, general and administrative	3,301				4,515				10,183			16,879

Total stock-based compensation expense	$	4,433			$	5,965			$	13,611		$	21,400


As of September 30, 2013, there was unrecognized compensation expense of $18.0 million related to stock options, and the Company expects to recognize this expense over a weighted average period of 2.84 years. As of September 30, 2013, there was unrecognized compensation expense of $5.3 million related to RSUs, and the Company expects to recognize this expenses over a weighted average period of 1.59 years.

Stock-based compensation expense for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant. Stock-based compensation expense for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards. The fair value of employee stock options was estimated using the following weighted-average assumptions:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2013			2012			2013			2012
Expected dividend yield	—	%		—	%		—	%		—	%
Risk-free interest rate	1.6	%		0.9	%		1.4	%		1.1	%
Expected term (in years)	6.1			5.9			6.1			6

Expected volatility	81	%		79	%		82	%		76	%

The fair value of nonemployee stock options was estimated using the following weighted-average assumptions:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2013			2012			2013			2012
Expected dividend yield	—	%		—	%		—	%		—	%
Risk-free interest rate	1.2	%		1.3	%		1.4	%		1.5	%
Expected term (in years)	4			6.9			5.3			7.1

Expected volatility	81	%		79	%		82	%		77	%

Related_Party_Transactions

Related Party Transactions	9 Months Ended
Related Party Transactions	Sep. 30, 2013
Related Party Transactions [Abstract]	'
Related Party Transactions	'
	Related Party Transactions

	February 2012 Private Placement

	In February 2012, the Company completed a private placement of 10,160,325 shares of its common stock at a price of $5.78 per share for aggregate proceeds of $58.7 million pursuant to a securities purchase agreement, among the Company and certain existing investors, including Total and Temasek, each a beneficial owner of more than 5% of the Company's existing common stock at the time of the transaction. In addition, members of the Board and certain parties related to such directors participated in the offering.

	May 2012 Private Placement

	In May 2012, the Company completed a private placement of 1,736,100 shares of its common stock at a price of $2.36 per share for aggregate proceeds of $4.1 million pursuant to a series of Common Stock Purchase Agreements, among the Company and members of the Board and certain parties related to such directors.

	March 2013 Private Placement

	In March 2013, the Company completed a private placement of 1,533,742 shares of its common stock to an existing stockholder, Biolding Investment SA ("Biolding"), at a price of $3.26 per share for aggregate proceeds of $5.0 million. This private placement represented the final tranche of Biolding's preexisting contractual obligation to fund $15.0 million upon satisfaction by the Company of certain criteria associated with the commissioning of the Company's production plant in Brotas, Brazil.

	Letter Agreement with Total

	In March 2013, the Company entered into a letter agreement with Total that reduced the conversion price of convertible promissory notes issuable under the Total Purchase Agreement, as described under “Related Party Convertible Notes” in Note 6, "Debt."

	Related Party Financings

	In June 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $10.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above under “Related Party Convertible Notes” in Note 6, “Debt."

	In July 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $20.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above under “Related Party Convertible Notes” in Note 6, “Debt."

	In August 2013, the Company entered into a securities purchase agreement by and among the Company, Total and Temasek, each a beneficial owner of more than 5% of the Company's existing common stock at the time of the transaction, for a private placement of convertible promissory notes in an aggregate principal amount of $73.0 million (see Note 1, "The Company"). The initial closing of the August 2013 Financing was completed in October 2013 (see Note 17, "Subsequent Events").

	In September 2013, the Company entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million as needed before the initial closing of the August 2013 Financing. The Company did not use this facility and it expired in October 2013 in accordance with its terms.

	In October 2013, the Company sold and issued a senior secured promissory note to Temasek for a bridge loan of $35.0 million. The note was due on February 2, 2014 and accrued interest at a rate of 5.5% each four months from October 4, 2013 (with a rate of 2% per month if a default occurred). The note was cancelled as payment for the investor’s purchase of the first tranche convertible note in the August 2013 Financing.

	Related Party Revenue

	The Company recognized related party product sales from Novvi for the three and nine months ended September 30, 2013, of $1.0 million and $1.1 million, respectively. For both the three months ended September 30, 2013 and 2012, the Company recorded zero and for the nine months ended September 30, 2013 and 2012, the Company recorded $2.6 million and zero, respectively, of revenue from the research and development activities that it has performed on behalf of Novvi. The related party accounts receivables from Novvi as of September 30, 2013 and December 31, 2012, was $1.1 million and zero, respectively.

	As a result of the July 2012 agreements with Total, the Company recognized related party collaboration revenue from Total for the three and nine months ended September 30 2012, of $9.8 million associated with the diesel and jet fuel research and development program.

Income_Taxes

Income Taxes	9 Months Ended
Income Taxes	Sep. 30, 2013
Income Tax Disclosure [Abstract]	'
Income Taxes	'
	Income Taxes

	For the three months ended September 30, 2013 and 2012, the Company recorded a benefit from income taxes of $1.4 million and provision for income taxes of $0.3 million, respectively, and a benefit from income taxes of $1.0 million and provision for income taxes of $0.8 million for the nine months ended September 30, 2013 and 2012, respectively. In September 2013, the Company entered into a letter agreement with Amyris Brasil Ltda., its wholly owned Brazilian subsidiary, agreeing to convert principal amount of approximately R$89.7 million (US$40.2 million based on the exchange rate as of September 30, 2013) of intercompany loans into equity in Amyris Brasil Ltda. The converted amount excluded accrued interest on the intercompany loan subject to conversion, and therefore the Company is no longer subject to potential withholding taxes on the loan interest. As a result, the Company recorded a tax benefit of approximately $1.6 million related to the reversal of previously accrued withholding taxes.

	Other than the above mentioned provision for income tax, no additional provision for income taxes has been made, net of the valuation allowance, due to cumulative losses since the commencement of operations.

	As of September 30, 2013, the US Internal Revenue Service (the "IRS") has completed its audit of the Company for tax year 2008 which concluded that there were no adjustments resulting from the audit. While the statutes are closed for tax year 2008, the US federal tax carryforwards (net operating losses and tax credits) may be adjusted by the IRS in the year in which the carryforward is utilized.

	In January 2013, the American Taxpayer Relief Act of 2012 (the "ATRA") was enacted. Under prior law, a taxpayer was entitled to a research tax credit for qualifying amounts incurred through December 31, 2011. The ATRA extends the research credit for two years for qualified research expenditures incurred through the end of 2013. The extension of the research credit is retroactive and includes amounts incurred after 2011. The benefit of the reinstated credit did not impact the income statement in the period of enactment, which is the first quarter of 2013, as the research and development credit carryforwards are offset by a full valuation allowance.

Segment_Information

Segment Information	9 Months Ended
	Sep. 30, 2013
Segment Reporting [Abstract]	'
Segment Information	'
	Segment Information

	The chief operating decision maker for the Company is the chief executive officer. The chief executive officer reviews financial information presented on a consolidated basis, accompanied by information about revenue by geographic region, for purposes of allocating resources and evaluating financial performance. The Company has one business activity comprised of research and development and sales of fuels and farnesene-derived products and there are no segment managers who are held accountable for operations, operating results or plans for levels or components below the consolidated unit level. Accordingly, the Company has determined that it has a single reportable segment and operating segment structure.

	Revenues by geography are based on the location of the customer. The following tables set forth revenue and long-lived assets by geographic area (in thousands):

	Revenues


		Three Months Ended September 30,				Nine Months Ended September 30,
		2013		2012		2013		2012
	United States	$	2,037	$	3,905	$	12,060	$	46,807

	Brazil	1,046		1,053		3,123		2,741

	Europe	2,829		12,452		7,059		15,785

	Asia	1,092		1,698		3,480		2,507

	Total	$	7,004	$	19,108	$	25,722	$	67,840


	Long-Lived Assets


		September 30,		December 31,
		2013		2012
	United States(1)	$	56,558	$	70,085

	Brazil(1)	82,649		91,170

	Europe	1,511		1,866

	Total	$	140,718	$	163,121



	-1	Certain reclassifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not change previously reported consolidated financial statements.

Comprehensive_Income_Loss_Note

Comprehensive Income (Loss) (Notes)	9 Months Ended
	Sep. 30, 2013
Equity [Abstract]	'
Comprehensive Income (Loss)	'
	Comprehensive Income (Loss)

	Comprehensive income (loss) represents all changes in stockholders’ equity except those resulting from investments or contributions by stockholders. The Company’s foreign currency translation adjustments represent the components of comprehensive income (loss) excluded from the Company’s net loss and have been disclosed in the condensed consolidated statements of comprehensive loss for all periods presented.

	The components of accumulated other comprehensive loss are as follows (in thousands):



		30-Sep-13			31-Dec-12
	Foreign currency translation adjustment, net of tax	$	(16,961	)	$	(12,807	)
	Total accumulated other comprehensive loss	$	(16,961	)	$	(12,807	)

Net_Loss_Attributable_to_Commo

Net Loss Attributable to Common Stockholders and Net Loss per Share (Notes)	9 Months Ended
	Sep. 30, 2013
Earnings Per Share [Abstract]	'
Net Loss Attributable to Common Stockholders and Net Loss per Share	'
	Net Loss Attributable to Common Stockholders and Net Loss per Share

	The Company computes net loss per share in accordance with ASC 260, “Earnings per Share.” Basic net loss per share of common stock is computed by dividing the Company’s net loss attributable to Amyris, Inc. common stockholders by the weighted average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units, common stock warrants, using the treasury stock method or the as converted method, as applicable. For all periods presented, basic net loss per share was the same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net loss are the same for each period presented.

	The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts):


		Three Months Ended September 30,							Nine Months Ended September 30,
		2013				2012			2013			2012
	Numerator:
	Net loss attributable to Amyris, Inc. common stockholders	$	(24,199	)		$	(20,293	)	$	(95,689	)	$	(161,647	)
	Denominator:
	Weighted average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	76,205,853				58,964,226			75,167,877			55,552,949
		76,205,853				58,964,226			75,167,877			55,552,949
	Net loss per share attributable to common stockholders, basic and diluted	$	(0.32	)		$	(0.34	)	$	(1.27	)	$	(2.91	)

	The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock for the periods presented because including them would have been anti-dilutive:


		Three and Nine Months Ended September 30,
		2013			2012
	Period-end stock options to purchase common stock	9,136,514			8,345,400
	Period-end stock options to purchase common stock	9,136,514			8,345,400
	Convertible promissory notes	20,110,650			11,077,785
	Convertible promissory notes	20,110,650			11,077,785
	Period-end common stock subject to repurchase	1			301
	Period-end common stock subject to repurchase	1			301
	Period-end common stock warrants	21,087			21,087
	Period-end common stock warrants	21,087			21,087
	Period-end restricted stock units	2,635,185			1,712,899
	Period-end restricted stock units	2,635,185			1,712,899
	Total	31,903,437			21,157,472
	Total	31,903,437			21,157,472

Subsequent_Events

Subsequent Events	9 Months Ended
Subsequent Events	Sep. 30, 2013
Subsequent Events [Abstract]	'
Subsequent Events	'
	Subsequent Events

	Total Amendment Agreement

	In October 2013, the Company entered into a letter agreement with Total relating to the Temasek Bridge Note and to the closing of the August 2013 Financing (the "Amendment Agreement"). In the August 2013 Financing, the Company was required to provide the purchasers under the August 2013 SPA with a security interest in the Company’s intellectual property if Total still held such security interest as of the initial closing of the August 2013 Financing. Under the terms of a previous Intellectual Property Security Agreement by and between the Company and Total (the "Security Agreement"), the Company had previously granted a security interest in favor of Total to secure the obligations of the Company under certain convertible promissory notes issued and issuable to Total under the Company’s purchase agreement with Total Purchase Agreement. The Security Agreement provides that such security interest will terminate if Total and the Company enter into certain agreements relating to the formation of the Fuels JV. To induce Total to (i) permit the Company to grant the security interest under the Temasek Bridge Note and the August 2013 Financing and (ii) waive a secured debt limitation contained in the outstanding convertible promissory notes held by Total (the “Total Securities”), the Company entered into the Amendment Agreement. Under the Amendment Agreement, the Company agreed to reduce, effective December 2, 2013, the conversion price for the Total Securities issued in 2012 (approximately $48.3 million of which are outstanding as of the date hereof) from $7.0682 per share to $2.20, the market price per share of the Company’s Common Stock as of the signing of the Amendment Agreement, as determined in accordance with applicable NASDAQ rules, unless the Company and Total enter into the JV Agreements on or prior to December 2, 2013.

	Related Party Financings

	In October 2013, the Company sold and issued the Temasek Bridge Note to Temasek for a bridge loan of $35.0 million. The Temasek Bridge Note was due on February 2, 2014 and accrued interest at a rate of 5.5% each four months from October 4, 2013. The note was cancelled on October 16, 2013 as payment for Temasek’s purchase of the first tranche convertible note in the August 2013 Financing.

	In October 2013, the Company amended the August 2013 SPA (see Note 1, "The Company") to include an additional cash investor in the first tranche convertible promissory notes in the principal amount of $7.6 million, and to proportionally increase the amount acquired through pro rata rights to $14.6 million ($9.2 million in the first tranche and up to $5.4 million in the second tranche). Also in October 2013, the Company completed the closing of the first tranche of the August 2013 Financing, issuing a total of $51.8 million in convertible promissory notes (the “Tranche I Notes”) for cash proceeds of $7.6 million and cancellation of outstanding convertible promissory notes of $44.2 million, of which $35.0 million resulted from cancellation of the Temasek Bridge Note. The Tranche I Notes are due sixty months from the date of issuance and will be convertible into the Company’s common stock at a conversion price equal to $2.44, subject to adjustment as described below. The Tranche I Notes are convertible at the option of the holder: (i) at any time after 18 months from the date of the August 2013 SPA, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. The conversion price of the Tranche I Notes will be reduced to $2.15 if a specified Company manufacturing plant fails to achieve a total production of 1.0 million liters within a run period of 45 days prior to June 30, 2014, the Company fails to achieve gross margins from product sales of at least 5% prior to June 30, 2014, or the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes. If either of the production and margin milestones occur, and in addition, the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes, the conversion price of the Tranche I Notes will be reduced to $1.87. Each Tranche I Note accrues interest from the date of issuance until the earlier of the date that such Tranche I Note is converted into the Company’s common stock or is repaid in full. Interest accrues at a rate of 5% per six months, compounded semiannually (with graduated interest rates of 6.5% applicable to the first 180 days and 8% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 6.5% for all other defaults). Interest for the first 30 months is payable in kind and added to the principal every six-months and thereafter, the Company may continue to pay interest in kind by adding to the principal every six-months or may elect to pay interest in cash. The Tranche I Notes may be prepaid by the Company after 30 months from the issuance date and initial interest payment; thereafter the Company has the option to prepay the Tranche I Notes every six months at the date of payment of the semi-annual coupon.

	The convertible promissory notes issuable in the second tranche of the August 2013 Financing (the “Tranche II Notes”) would be due 5 years after the date of the issuance of the first Tranche II Notes and would be subject to a conversion price equal to $2.87, subject to adjustment as described below. Specifically, the Tranche II Notes would be convertible at the option of the holder (i) at any time 12 months after issuance, (ii) on a change of control of the Company, and (iii) upon the occurrence of an event of default. Each Tranche II Notes will accrue interest from the date of issuance until the earlier of the date that such Tranche II Notes is converted into the Company's common stock or repaid in full. Interest will accrue at a rate per annum equal to 10%, compounded annually (with graduated interest rates of 13% applicable to the first 180 days and 16% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at a rate equal to 12% for all other defaults). Interest for the first 36 months shall be payable in kind and added to the principal every year following the issue date and thereafter, the Company may continue to pay interest in kind by adding to the principal on every year anniversary of the issue date or may elect to pay interest in cash.

	In addition to the conversion price adjustments set forth above, the conversion prices of the Tranche I Notes and Tranche II Notes are subject to further adjustment (i) according to proportional adjustments to outstanding common stock of the Company in case of certain dividends and distributions, (ii) according to anti-dilution provisions, and (iii) with respect to notes held by any purchaser other than Total, in the event that Total exchanges existing convertible notes for new securities of the Company in connection with future financing transactions in excess of its pro rata amount. Notwithstanding the foregoing, holders of a majority of the principal amount of the notes outstanding at the time of conversion may waive any anti-dilution adjustments to the conversion price. The purchasers have a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if the purchasers do not require such repayment. The August 2013 SPA, Tranche I Notes and Tranche II Notes include covenants regarding payment of interest, maintenance of the Company’s listing status, limitations on debt and on certain liens, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the August 2013 SPA, Tranche I Notes and Tranche II Notes, with default interest rates and associated cure periods applicable to the covenant regarding SEC reporting.

Summary_of_Significant_Account1

Summary of Significant Accounting Policies (Policies)	9 Months Ended
Summary of Significant Accounting Policies (Policies)	Sep. 30, 2013
Accounting Policies [Abstract]	'
Basis of Accounting, Policy [Policy Text Block]	'
	Basis of Presentation

	The accompanying interim condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (“GAAP”) and with the instructions for Form 10-Q and Regulation S-X. Accordingly, they do not include all of the information and notes required for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Form 10-K filed with the Securities and Exchange Commission (“SEC”) on March 28, 2013. The unaudited condensed consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.
	Unaudited Interim Financial Information

	The accompanying interim condensed consolidated financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual consolidated financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the results of operations for the periods presented. The year-end condensed consolidated balance sheet data was derived from audited financial statements, but does not include all disclosures required by GAAP. The condensed consolidated results of operations for any interim period are not necessarily indicative of the results to be expected for the full year or for any other future year or interim period.
Use of Estimates [Policy Text Block]	'
	Use of Estimates

	In preparing the unaudited condensed consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the unaudited condensed consolidated financial statements and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.
New Accounting Pronouncements, Policy [Policy Text Block]	'
	Recent Accounting Pronouncements

	In December 2011, the International Accounting Standards Board and the Financial Accounting Standards Board ("FASB") issued common disclosure requirements that are intended to enhance comparability between financial statements prepared on the basis of GAAP and those prepared in accordance with International Financial Reporting Standards. In January 2013, the FASB issued an accounting standard update to limit the scope of the new balance sheet offsetting disclosures to derivative instruments, repurchase agreements, and securities lending transactions to the extent that they are offset in the financial statement or subject to an enforceable master netting arrangement or similar arrangement. While this guidance does not change existing offsetting criteria in GAAP or the permitted balance sheet presentation for items meeting the criteria, it requires an entity to disclose both net and gross information about assets and liabilities that have been offset and the related arrangements. Required disclosures under this new guidance should be provided retrospectively for all comparative periods presented. This new guidance is effective for fiscal years beginning on or after January 1, 2013, and interim periods within those years. The adoption of this guidance in the Company's first quarter of fiscal year 2013 did not have a material effect on the Company's consolidated financial statements.

	In July 2012, the FASB issued an amended accounting standard update to simplify how entities test indefinite-lived intangible assets for impairment which improve consistency in impairment testing requirements among long-lived asset categories. The amended guidance permits an assessment of qualitative factors to determine whether it is more likely than not that the fair value of an indefinite-lived intangible asset is less than its carrying value. For assets in which this assessment concludes it is more likely than not that the fair value is more than its carrying value, then the amended guidance eliminates the requirement to perform quantitative impairment testing as outlined in the previously issued standards. The amended guidance is effective for fiscal years beginning after September 15, 2012 and early adoption is permitted. The adopted and amended guidance did not have an impact on the Company's consolidated financial statements.

	In February 2013, in connection with the accounting standard related to the presentation of the statement of comprehensive income, the FASB issued an accounting standard update to improve the reporting of reclassifications out of accumulated other comprehensive income of various components. This guidance requires companies to present either parenthetically on the face of the financial statements or in the notes, significant amounts reclassified from each component of accumulated other comprehensive income and the income statement line items affected by the reclassification. This standard is effective for interim periods and fiscal years beginning after December 15, 2012. The adoption of this guidance in the Company's first quarter of fiscal year 2013 did not have a material effect on the Company's consolidated financial statements.

	In July 2013, the FASB issued a new accounting standard update on the financial statement presentation of unrecognized tax benefits. The new guidance provides that a liability related to an unrecognized tax benefit would be presented as a reduction of a deferred tax asset for a net operating loss carryforward, a similar tax loss or a tax credit carryforward if such settlement is required or expected in the event the uncertain tax position is disallowed. The new guidance becomes effective for the Company on January 1, 2014 and will be applied prospectively to unrecognized tax benefits that exist at the effective date with retrospective applications permitted. The Company is currently assessing the impact of this new guidance.

Fair_Value_of_Financial_Instru1

Fair Value of Financial Instruments (Tables)	9 Months Ended
	Sep. 30, 2013
Fair Value Disclosures [Abstract]	'
Schedule of Fair Value, Assets and Liabilities Measured on Recurring Basis [Table Text Block]	'
	As of September 30, 2013, the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):


		Level 1				Level 2				Level 3				Balance as of
														30-Sep-13
	Financial Assets
	Money market funds	$	245			$	—			$	—			$	245

	Certificates of deposit	580				—				—				580

	Total financial assets	$	825			$	—			$	—			$	825

	Financial Liabilities
	Loans payable(1)	$	—			$	19,502			$	—			$	19,502

	Credit facilities(1)	—				8,555				—				8,555

	Convertible notes(1)	—				—				88,261				88,261

	Compound embedded derivative liability	—				—				13,836				13,836

	Currency interest rate swap derivative liability	—				3,074				—				3,074

	Total financial liabilities	$	—			$	31,131			$	102,097			$	133,228


	______________
	(1) These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis.

	The Company’s financial assets and financial liabilities as of December 31, 2012 are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):



		Level 1				Level 2				Level 3				Balance as of December 31, 2012
	Financial Assets
	Money market funds	$	15,847			$	—			$	—			$	15,847

	Certificates of deposit	757				—				—				757

	Total financial assets	$	16,604			$	—			$	—			$	16,604

	Financial Liabilities
	Notes payable(1)	$	—			$	1,676			$	—			$	1,676

	Loans payable(1)	—				20,707				—				20,707

	Credit facilities(1)	—				11,503				—				11,503

	Convertible notes(1)	—				—				62,522				62,522

	Compound embedded derivative liability	—				—				7,894				7,894

	Currency interest rate swap derivative liability	—				1,367				—				1,367

	Total financial liabilities	$	—			$	35,253			$	70,416			$	105,669


	______________
	(1) These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis.
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Table Text Block]	'
	The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liability measured at fair value using significant unobservable inputs (Level 3) (in thousands):


		Compound Embedded Derivative Liability
	Balance at December 31, 2012	$	7,894

	Transfers in to Level 3	13,076

	Total (gain) losses included in other income (expense), net	(7,134		)
	Balance at September 30, 2013	$	13,836

Schedule of Derivative Instruments in Statement of Financial Position, Fair Value [Table Text Block]	'
	Derivative instruments measured at fair value as of September 30, 2013 and December 31, 2012, and their classification on the condensed consolidated balance sheet and condensed consolidated statements of operations, are presented in the following tables (in thousands except contract amounts):


			Asset/Liability as of
			30-Sep-13							31-Dec-12
	Type of Derivative Contract		Quantity of			Fair Value				Quantity of			Fair Value
			Contracts							Contracts
	Currency interest rate swap, included as net liability in other liabilities		1			$	3,074			1			$	1,367

Schedule of Derivative Instruments, Gain (Loss) in Statement of Financial Performance [Table Text Block]	'


	Type of Derivative Contract		Income	Three Months Ended September 30,								Nine Months Ended September 30,
			Statement Classification	2013				2012				2013				2012
				Gain (Loss) Recognized								Gain (Loss) Recognized
	Regulated fixed price futures contracts		Cost of products sold	$	—			$	(31	)		$	—			$	(288	)

	Currency interest rate swap		Other income (expense), net	$	(137	)		$	82			$	(1,707	)		$	(1,133	)

Balance_Sheet_Components_Table

Balance Sheet Components (Tables)	9 Months Ended
	Sep. 30, 2013
Balance Sheet Components [Abstract]	'
Schedule of Inventory, Current [Table Text Block]	'
	Inventories

	Inventories are stated at the lower of cost or market and consist of the following (in thousands):


		September 30,				December 31,
		2013				2012
	Raw materials	$	1,527			$	1,574

	Work-in-process	5,218				1,771

	Finished goods	1,203				2,689

	Inventories, net	$	7,948			$	6,034

Deferred Costs, Capitalized, Prepaid, and Other Assets Disclosure [Table Text Block]	'
	Prepaid and Other Current Assets

	Prepaid and other current assets is comprised of the following (in thousands):


		September 30,				December 31,
		2013				2012
	Advances to contract manufacturers(1)	$	10			$	784

	Manufacturing catalysts	1,441				1,895

	Recoverable VAT and other taxes	4,146				4,167

	Other	1,567				2,079

	Prepaid and other current assets	$	7,164			$	8,925

	____

	-1	At December 31, 2012, the amount of $0.8 million, relates to the current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization was offset against purchases of inventory during 2013.
Property, Plant and Equipment [Table Text Block]	'
	Property, Plant and Equipment, net

	Property, plant and equipment, net is comprised of the following (in thousands):


				September 30,				December 31,
		Useful Life		2013				2012
	Leasehold improvements	Lesser of remaining useful life or lease term		$	39,114			$	39,290

	Machinery and equipment	7 - 15 Years		98,350				105,162

	Computers and software	3 - 5 Years		8,509				8,232

	Furniture and office equipment	5 years		2,520				2,467

	Buildings	15 Years		6,829				5,888

	Vehicles	5 years		465				575

	Construction in progress			42,933				45,372

				198,720				206,986

	Less: accumulated depreciation and amortization			(58,002		)		(43,865		)
	Property, plant and equipment, net			$	140,718			$	163,121

Schedule of Other Assets, Noncurrent [Table Text Block]	'
	Other Assets

	Other assets are comprised of the following (in thousands):


		September 30,				December 31,
		2013				2012

	Deposits on property and equipment, including taxes	$	2,137			$	2,363

	Advances to contract manufacturers, net of current portion(1)	—				2,222

	Recoverable taxes on purchased property, plant and equipment and inventory(2)	15,609				13,597

	Other	1,979				1,930

	Total other assets	$	19,725			$	20,112

	_________

	(1)	At December 31, 2012, the amount of $2.2 million relates to the non-current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization was offset against purchases of inventory during 2013.

	(2)	At September 30, 2013 and December 31, 2012, the amounts of $15.6 million and $13.6 million, respectively, are recoverable taxes from Brazilian governmental entities.
Schedule of Accrued Liabilities [Table Text Block]	'
	Accrued and Other Current Liabilities

	Accrued and other current liabilities are comprised of the following (in thousands):


		September 30,				December 31,
		2013				2012

	Professional services	$	2,859			$	824

	Accrued vacation	2,179				2,673

	Payroll and related expenses	5,099				5,809

	Tax-related liabilities	641				851

	Deferred rent, current portion	1,111				1,448

	Accrued interest(1)	1,435				965

	Contractual obligations to contract manufacturers, current	5,868				9,952

	Customer advances	372				970

	Other(1)	741				918

	Total accrued and other current liabilities	$	20,305			$	24,410

	__________

	(1)	Certain reclassifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Commitments_and_Contingencies_

Commitments and Contingencies (Tables)	9 Months Ended
	Sep. 30, 2013
Commitments and Contingencies Disclosure [Abstract]	'
Schedule of Future Minimum Payments For Lease Obligations [Table Text Block]	'
	Future minimum payments under the Company's lease obligations as of September 30, 2013, are as follows (in thousands):



	Years ending December 31:	Capital			Operating		Total Lease Obligations
		Leases			Leases
	2013 (Remaining Three Months)	$	274		$	1,477	$	1,751

	2014	1,007			6,277		7,284

	2015	289			6,581		6,870

	2016	—			6,595		6,595

	2017	—			6,585		6,585

	Thereafter	—			38,973		38,973

	Total future minimum lease payments	1,570			$	66,488	$	68,058

	Less: amount representing interest	(75		)

	Present value of minimum lease payments	1,495

	Less: current portion	(1,031		)

	Long-term portion	$	464

Debt_Tables

Debt (Tables)	9 Months Ended
	Sep. 30, 2013
Debt Disclosure [Abstract]	'
Schedule of Debt [Table Text Block]	'
	Debt is comprised of the following (in thousands):



		September 30,			December 31,
		2013			2012
	Credit facilities	$	9,750		$	12,409

	Notes payable	—			1,572

	Convertible notes	25,000			25,000

	Related party convertible notes	58,091			39,033

	Loans payable	25,997			26,150

	Total debt	118,838			104,164

	Less: current portion	(5,448		)	(3,325		)
	Long-term debt	$	113,390		$	100,839

Schedule of Long-term Debt Instruments [Table Text Block]	'

	Future minimum payments under the debt agreements as of September 30, 2013 are as follows (in thousands):



	Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Loans Payable			Credit Facility
	2013 (Remaining three months)	$	—		$	192		$	492		$	682

	2014	—			760			5,243			2,681

	2015	—			765			4,042			2,542

	2016	—			761			3,887			2,404

	2017	83,267			25,125			3,726			2,264

	Thereafter	—			—			15,052			579

	Total future minimum payments	83,267			27,603			32,442			11,152

	Less: amount representing interest(1)	(25,176		)	(2,603		)	(6,445		)	(1,402		)
	Present value of minimum debt payments	58,091			25,000			25,997			9,750

	Less: current portion	—			—			(3,286		)	(2,162		)

	Noncurrent portion of debt	$	58,091		$	25,000		$	22,711		$	7,588


	(1) Including debt discount of $20.2 million associated with the related party convertible debt.

Joint_Ventures_and_Noncontroll1

Joint Ventures and Noncontrolling Interest (Tables)	9 Months Ended
	Sep. 30, 2013
Joint Ventures and Noncontrolling Interest [Abstract]	'
Schedule of Variable Interest Entities [Table Text Block]	'
	The table below reflects the carrying amount of the assets and liabilities of the two consolidated VIEs for which the Company is the primary beneficiary. As of September 30, 2013, the assets include $22.7 million in property, plant and equipment, $4.1 million in other assets and $0.4 million in current assets. The liabilities include $0.2 million in accounts payable and accrued current liabilities and $0.1 million in loan obligations by Glycotech to its shareholders that are non-recourse to the Company. The creditors of each consolidated VIE have recourse only to the assets of that VIE.




		September 30,			December 31,
	(In thousands)	2013			2012
	Assets	$	27,118		$	29,564

	Liabilities	$	335		$	355

Noncontrolling Interest [Table Text Block]	'
	The change in noncontrolling interest for the nine months ended September 30, 2013 and 2012 is summarized below (in thousands):


		2013			2012
	Balance at January 1	$	(877	)	$	(240	)
	Foreign currency translation adjustment	55			209

	Gain (loss) attributable to noncontrolling interest	232			(772		)

	Balance at September 30	$	(590	)	$	(803	)

Goodwill_and_Intangible_Assets1

Goodwill and Intangible Assets (Tables)	9 Months Ended
	Sep. 30, 2013
Goodwill and Intangible Assets Disclosure [Abstract]	'
Schedule of Intangible Assets and Goodwill [Table Text Block]	'
	The following table presents the components of the Company's intangible assets (in thousands):



				30-Sep-13								31-Dec-12
		Useful Life in Years		Gross Carrying Amount		Accumulated Amortization			Net Carrying Value			Gross Carrying Amount			Accumulated Amortization			Net Carrying Value
	In-process research and development	Indefinite		$	8,560	$	—		$	8,560		$	8,560		$	—		$	8,560

	Acquired licenses and permits	2		772		(772		)	—			772			(740		)	32

	Goodwill	Indefinite		560		—			560			560						560

				$	9,892	$	(772	)	$	9,120		$	9,892		$	(740	)	$	9,152


	The following table presents the activity of intangible assets for the nine months ended September 30, 2013 (in thousands):



			31-Dec-12														30-Sep-13
			Net Carrying Value			Additions				Adjustments			Amortization				Net Carrying Value
	In-process research and development		$	8,560		$	—			$	—		$	—			$	8,560

	Acquired licenses and permits		32			—				—			(32		)		—

	Goodwill		560			—				—			—				560

			$	9,152		$	—			$	—		$	(32	)		$	9,120

StockBased_Compensation_Plans_

Stock-Based Compensation Plans (Tables)	9 Months Ended
	Sep. 30, 2013
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'
Schedule of Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity [Table Text Block]	'
	The Company’s stock option activity and related information for the nine months ended September 30, 2013 was as follows:



				Number			Weighted Average				Weighted		Aggregate
				Outstanding			Exercise				Average		Intrinsic
							Price				Remaining		Value
											Contractual
											Life (Years)
													(in thousands)
	Outstanding - December 31, 2012			8,946,592			$	9.07			7.5		$	954

		Options granted		2,772,130			$	2.83

		Options exercised		(193,166	)		$	0.87

		Options cancelled		(2,389,042	)		$	9.56

	Outstanding - September 30, 2013			9,136,514			$	7.23			7.72		$	71


	Vested and expected to vest after September 30, 2013			8,454,008			$	7.44			7.61		$	71

	Exercisable at September 30, 2013			3,950,398			$	9.7			6.18		$	71

Schedule of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity [Table Text Block]	'
	The Company’s restricted stock units ("RSUs") and restricted stock activity and related information for the nine months ended September 30, 2013 was as follows:



			RSUs			Weighted Average Grant-Date Fair Value				Weighted Average Remaining Contractual Life (Years)
	Outstanding - December 31, 2012		2,550,799			$	7.92			1.3

		Awarded	1,100,000			$	2.84			—

		Vested	(654,619	)		$	5.91			—

		Forfeited	(360,995	)		$	3.92			—

	Outstanding - September 30, 2013		2,635,185			$	4.2			1.05

	Expected to vest after September 30, 2013		2,389,722			$	4.2			0.98

Schedule of Share-based Compensation, Shares Authorized under Stock Option Plans, by Exercise Price Range [Table Text Block]	'
	The following table summarizes information about stock options outstanding as of September 30, 2013:




		Options Outstanding									Options Exercisable
	Exercise Price	Number of Options			Weighted Average		Weighted Average Exercise Price				Number of Options			Weighted Average Exercise Price
					Remaining Contractual Life
					(Years)
	$0.10—$2.76	1,218,972			8.34		$	2.63			248,047			$	2.31

	$2.79—$2.85	964,895			9.75		$	2.79			68			$	2.85

	$2.87—$2.87	917,000			9.67		$	2.87			—			$	—

	$2.89—$3.12	918,271			9.14		$	2.99			204,297			$	3.04

	$3.23—$3.83	189,639			8.79		$	3.31			86,438			$	3.39

	$3.86—$3.86	1,045,052			8.16		$	3.86			416,769			$	3.86

	$3.93—$4.06	992,731			4.25		$	3.95			926,064			$	3.94

	$4.31—$14.28	919,609			6.11		$	6.8			748,254			$	6.38

	$16.00—$19.61	942,063			7.05		$	16.31			600,610			$	16.29

	$20.41—$30.17	1,028,282			6.84		$	23.86			719,851			$	23.62

	$0.10—$30.17	9,136,514			7.72		$	7.23			3,950,398			$	9.7

Schedule of Service Share-based Compensation, Allocation of Recognized Period Costs [Table Text Block]	'
	Stock-based compensation expense related to options and restricted stock units granted to employees and nonemployees was allocated to research and development expense and sales, general and administrative expense as follows (in thousands):



		Three Months Ended September 30,								Nine Months Ended September 30,
		2013				2012				2013				2012
	Research and development	$	1,132			$	1,450			$	3,428			$	4,521

	Sales, general and administrative	3,301				4,515				10,183				16,879

	Total stock-based compensation expense	$	4,433			$	5,965			$	13,611			$	21,400

Employee Share Based Compensation [Member]	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'
Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions [Table Text Block]	'
	Stock-based compensation expense for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant. Stock-based compensation expense for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards. The fair value of employee stock options was estimated using the following weighted-average assumptions:



		Three Months Ended September 30,						Nine Months Ended September 30,
		2013			2012			2013			2012
	Expected dividend yield	—	%		—	%		—	%		—	%
	Risk-free interest rate	1.6	%		0.9	%		1.4	%		1.1	%
	Expected term (in years)	6.1			5.9			6.1			6

	Expected volatility	81	%		79	%		82	%		76	%
Non Employee Share Based Compensation [Member]	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'
Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions [Table Text Block]	'
	The fair value of nonemployee stock options was estimated using the following weighted-average assumptions:



		Three Months Ended September 30,						Nine Months Ended September 30,
		2013			2012			2013			2012
	Expected dividend yield	—	%		—	%		—	%		—	%
	Risk-free interest rate	1.2	%		1.3	%		1.4	%		1.5	%
	Expected term (in years)	4			6.9			5.3			7.1

	Expected volatility	81	%		79	%		82	%		77	%

Segment_Information_Tables

Segment Information (Tables)	9 Months Ended
	Sep. 30, 2013
Segment Reporting [Abstract]	'
Schedule of Revenue from External Customers and Long-Lived Assets, by Geographical Areas [Table Text Block]	'
	Revenues by geography are based on the location of the customer. The following tables set forth revenue and long-lived assets by geographic area (in thousands):

	Revenues


		Three Months Ended September 30,				Nine Months Ended September 30,
		2013		2012		2013		2012
	United States	$	2,037	$	3,905	$	12,060	$	46,807

	Brazil	1,046		1,053		3,123		2,741

	Europe	2,829		12,452		7,059		15,785

	Asia	1,092		1,698		3,480		2,507

	Total	$	7,004	$	19,108	$	25,722	$	67,840


	Long-Lived Assets


		September 30,		December 31,
		2013		2012
	United States(1)	$	56,558	$	70,085

	Brazil(1)	82,649		91,170

	Europe	1,511		1,866

	Total	$	140,718	$	163,121



	-1	Certain reclassifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not change previously reported consolidated financial statements.

Comprehensive_Income_Loss_Tabl

Comprehensive Income (Loss) (Tables)	9 Months Ended
Comprehensive Income (Loss) (Tables)	Sep. 30, 2013
Equity [Abstract]	'
Schedule of Accumulated Other Comprehensive Loss	'
	The components of accumulated other comprehensive loss are as follows (in thousands):



		30-Sep-13			31-Dec-12
	Foreign currency translation adjustment, net of tax	$	(16,961	)	$	(12,807	)
	Total accumulated other comprehensive loss	$	(16,961	)	$	(12,807	)

Net_Loss_Attributable_to_Commo1

Net Loss Attributable to Common Stockholders and Net Loss per Share (Tables)	9 Months Ended
	Sep. 30, 2013
Earnings Per Share [Abstract]	'
Schedule of Calculation of Numerator and Denominator in Earnings Per Share [Table Text Block]	'
	The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts):


		Three Months Ended September 30,							Nine Months Ended September 30,
		2013				2012			2013			2012
	Numerator:
	Net loss attributable to Amyris, Inc. common stockholders	$	(24,199	)		$	(20,293	)	$	(95,689	)	$	(161,647	)
	Denominator:
	Weighted average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	76,205,853				58,964,226			75,167,877			55,552,949
		76,205,853				58,964,226			75,167,877			55,552,949
	Net loss per share attributable to common stockholders, basic and diluted	$	(0.32	)		$	(0.34	)	$	(1.27	)	$	(2.91	)
Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share [Table Text Block]	'
	The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock for the periods presented because including them would have been anti-dilutive:


		Three and Nine Months Ended September 30,
		2013			2012
	Period-end stock options to purchase common stock	9,136,514			8,345,400
	Period-end stock options to purchase common stock	9,136,514			8,345,400
	Convertible promissory notes	20,110,650			11,077,785
	Convertible promissory notes	20,110,650			11,077,785
	Period-end common stock subject to repurchase	1			301
	Period-end common stock subject to repurchase	1			301
	Period-end common stock warrants	21,087			21,087
	Period-end common stock warrants	21,087			21,087
	Period-end restricted stock units	2,635,185			1,712,899
	Period-end restricted stock units	2,635,185			1,712,899
	Total	31,903,437			21,157,472
	Total	31,903,437			21,157,472

The_Company_Details

The Company (Details) (USD $)

3 Months Ended

9 Months Ended

3 Months Ended

1 Months Ended

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Dec. 31, 2012

Sep. 30, 2013

Aug. 31, 2013

Sep. 30, 2013

Aug. 31, 2013

Oct. 31, 2013

Oct. 16, 2013

Aug. 31, 2013

Oct. 31, 2013

Aug. 31, 2013

Oct. 31, 2013

Tate & Lyle Termination Agreement [Member]

August 2013 Convertible Notes [Member]

Maximum [Member]

Subsequent Event [Member]

First Tranche [Member]

Second Tranche [Member]

August 2013 Convertible Notes [Member]

Temasek Bridge Note [Member]

Maximum [Member]

August 2013 Convertible Notes [Member]

Subsequent Event [Member]

August 2013 Convertible Notes [Member]

Subsequent Event [Member]

Cancellation of the Temasek Bridge Note [Member]

August 2013 Convertible Notes [Member]

Loss on purchase commitments and write off of production assets

$1,438,000

$8,423,000

$38,090,000

$8,400,000

Expected Capital Expenditures During Current Fiscal Year

10,000,000

Retained Earnings (Accumulated Deficit)

-682,016,000

-586,327,000

Cash, Cash Equivalents, and Short-term Investments

6,300,000

Long-term Debt

118,838,000

104,164,000

Debt, current portion

5,448,000

3,325,000

Debt Instrument, Face Amount

73,000,000

51,800,000

42,600,000

30,400,000

Private Placement Convertible Notes, Period

'24 months

Future Proceeds from Convertible Debt

60,000,000

35,000,000

25,000,000

Future Cancellation Of Debt, Amount

13,000,000

44,200,000

35,000,000

7,600,000

5,400,000

Bridge Loan

5,000,000

35,000,000

Debt Instrument, Interest Rate, Stated Percentage

5.50%

Debt Instrument, Amended Additional Investor Amount

7,600,000

Debt Instrument, Amended Promissory Note, Amount

$14,600,000

$9,200,000

$5,400,000

Fair_Value_of_Financial_Instru2

Fair Value of Financial Instruments, Hierarchy (Details) (Fair Value, Measurements, Recurring [Member], USD $)	Sep. 30, 2013		Dec. 31, 2012
In Thousands, unless otherwise specified	Sep. 30, 2013		Dec. 31, 2012
Quoted Prices in Active Markets for Identical Assets (Level 1) [Member]	'		'
Financial Assets [Abstract]	'		'
Money market funds	$245		$15,847
Certificates of deposit	580		757
Total financial assets	825		16,604
Financial Liabilities [Abstract]	'		'
Notes payable	'		0	[1]
Loans payable(1)	0	[1]	0	[1]
Credit facilities(1)	0	[1]	0	[1]
Convertible notes(1)	0	[1]	0	[1]
Compound embedded derivative liability	0		0
Currency interest rate swap derivative liability	0		0
Total financial liabilities	0		0
Other Observable Inputs (Level 2) [Member]	'		'
Financial Assets [Abstract]	'		'
Money market funds	0		0
Certificates of deposit	0		0
Total financial assets	0		0
Financial Liabilities [Abstract]	'		'
Notes payable	'		1,676	[1]
Loans payable(1)	19,502	[1]	20,707	[1]
Credit facilities(1)	8,555	[1]	11,503	[1]
Convertible notes(1)	0	[1]	0	[1]
Compound embedded derivative liability	0		0
Currency interest rate swap derivative liability	3,074		1,367
Total financial liabilities	31,131		35,253
Significant Unobservable Inputs (Level 3) [Member]	'		'
Financial Assets [Abstract]	'		'
Money market funds	0		0
Certificates of deposit	0		0
Total financial assets	0		0
Financial Liabilities [Abstract]	'		'
Notes payable	'		0	[1]
Loans payable(1)	0	[1]	0	[1]
Credit facilities(1)	0	[1]	0	[1]
Convertible notes(1)	88,261	[1]	62,522	[1]
Compound embedded derivative liability	13,836		7,894
Currency interest rate swap derivative liability	0		0
Total financial liabilities	102,097		70,416
Balance as of March 31 [Member]	'		'
Financial Assets [Abstract]	'		'
Money market funds	245		15,847
Certificates of deposit	580		757
Total financial assets	825		16,604
Financial Liabilities [Abstract]	'		'
Notes payable	'		1,676	[1]
Loans payable(1)	19,502	[1]	20,707	[1]
Credit facilities(1)	8,555	[1]	11,503	[1]
Convertible notes(1)	88,261	[1]	62,522	[1]
Compound embedded derivative liability	13,836		7,894
Currency interest rate swap derivative liability	3,074		1,367
Total financial liabilities	$133,228		$105,669

[1]	These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis.

Fair_Value_Measurements_Fair_V

Fair Value Measurements Fair Value Using Significant Unobservable Inputs (Level 3) (Details) (Derivative Liability - Compound Embedded Derivatives [Member], USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013
Derivative Liability - Compound Embedded Derivatives [Member]	'
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]	'
Fair value, beginning of period	$7,894
Transfers in to Level 3	13,076
Change in fair value recorded in other income (expense), net	-7,134
Fair value, end of period	$13,836

Fair_Value_of_Financial_Instru3

Fair Value of Financial Instruments, Derivative Disclosures (Details) (Not Designated as Hedging Instrument [Member], USD $)	3 Months Ended		9 Months Ended				3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Dec. 31, 2012	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
	Future [Member]	Future [Member]	Future [Member]	Future [Member]	Future [Member]	Future [Member]	Currency interest rate swap [Member]	Currency interest rate swap [Member]	Currency interest rate swap [Member]	Currency interest rate swap [Member]
	Cost of products sold [Member]	Cost of products sold [Member]	Cost of products sold [Member]	Cost of products sold [Member]	Currency interest rate swap, included as net liability in other long term liability [Member]	Currency interest rate swap, included as net liability in other long term liability [Member]	Other income (expense), net [Member]	Other income (expense), net [Member]	Other income (expense), net [Member]	Other income (expense), net [Member]
					Contracts	Contracts
Derivative [Line Items]	'	'	'	'	'	'	'	'	'	'
Quantity of Contracts (in contracts)	'	'	'	'	1	1	'	'	'	'
Fair Value	'	'	'	'	$3,074	$1,367	'	'	'	'
Derivative contracts, gain (loss)	$0	($31)	$0	($288)	'	'	($137)	$82	($1,707)	($1,133)

Fair_Value_of_Financial_Instru4

Fair Value of Financial Instruments Fair Value of Financial Instruments, Textuals (Details)	Jul. 13, 2012	Sep. 30, 2012	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Dec. 31, 2012
	Banco Pine July 2012 Loan Agreement [Member]	Bridge Loan [Member]	Bridge Loan [Member]	Interest Rate Swap [Member]	Interest Rate Swap [Member]	Derivative Liability - Compound Embedded Derivatives [Member]	Derivative Liability - Compound Embedded Derivatives [Member]
	BRL	Banco Pine S.A Loan Agreement June 2012 [Member]	Banco Pine S.A Loan Agreement June 2012 [Member]	Banco Pine July 2012 Loan Agreement [Member]	Banco Pine July 2012 Loan Agreement [Member]	USD ($)	USD ($)
		USD ($)	BRL	USD ($)	BRL
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'	'	'	'	'	'
Debt Instrument, Face Amount	22,000,000	$25,600,000	52,000,000	'	'	'	'
Notional Amount of Interest Rate Derivatives	'	'	'	9,900,000	22,000,000	'	'
Derivative, Fixed Interest Rate	'	'	'	'	3.94%	'	'
Fair Value, Measurement with Unobservable Inputs Reconciliations, Recurring Basis, Liability Value	'	'	'	'	'	$13,836,000	$7,894,000

Balance_Sheet_Components_Inven

Balance Sheet Components Inventory (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified	Sep. 30, 2013	Dec. 31, 2012
Balance Sheet Components [Abstract]	'	'
Raw materials	$1,527	$1,574
Work-in-process	5,218	1,771
Finished goods	1,203	2,689
Inventories, net	$7,948	$6,034

Balance_Sheet_Components_Prepa

Balance Sheet Components Prepaid and Other Current Assets (Details) (USD $)	Sep. 30, 2013		Dec. 31, 2012
In Thousands, unless otherwise specified	Sep. 30, 2013		Dec. 31, 2012
Balance Sheet Components [Abstract]	'		'
Advances to contract manufacturers	$10	[1]	$784	[1]
Manufacturing catalysts	1,441		1,895
Recoverable VAT and other taxes	4,146		4,167
Other	1,567		2,079
Prepaid and other current assets	$7,164		$8,925

[1]	At December 31, 2012, the amount of $0.8 million, relates to the current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization was offset against purchases of inventory during 2013.

Balance_Sheet_Components_Prope

Balance Sheet Components Property, Plant and Equipment, net (Details)

1 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

Dec. 31, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

USD ($)

BRL

USD ($)

BRL

USD ($)

Capital Lease Obligations [Member]

Leasehold improvements [Member]

Machinery and equipment [Member]

Computer and software [Member]

Furniture and office equipment [Member]

Buildings [Member]

Vehicles [Member]

Construction in progress [Member]

Machinery and Equipment and Furniture and Office Equipment Under Capital Lease [Member]

Property Plant and Equipment Including Capital Leases [Member]

Minimum [Member]

Maximum [Member]

USD ($)

Capital Lease Obligations [Member]

USD ($)

Machinery and equipment [Member]

Computer and software [Member]

Machinery and equipment [Member]

Computer and software [Member]

USD ($)

Property, Plant and Equipment [Line Items]

Property, Plant and Equipment, Gross

$206,986,000

$198,720,000

$39,114,000

$39,290,000

$98,350,000

$105,162,000

$8,509,000

$8,232,000

$2,520,000

$2,467,000

$6,829,000

$5,888,000

$465,000

$575,000

$42,933,000

$45,372,000

$3,400,000

$9,100,000

Less: accumulated depreciation and amortization

-43,865,000

-58,002,000

-1,300,000

-4,100,000

Property, plant and equipment, net

163,121,000

140,718,000

Depreciation and amortization

12,259,000

10,686,000

3,800,000

3,100,000

12,200,000

10,400,000

Interest Costs Capitalized

$600,000

1,100,000

$500,000

1,100,000

Property, Plant and Equipment, Useful Life

'5 years

'15 years

'5 years

'7 years

'3 years

'15 years

'5 years

Balance_Sheet_Components_Other

Balance Sheet Components Other assets (Details) (USD $)	Sep. 30, 2013		Dec. 31, 2012
In Thousands, unless otherwise specified	Sep. 30, 2013		Dec. 31, 2012
Balance Sheet Components [Abstract]	'		'
Deposits on property and equipment, including taxes	$2,137		$2,363
Advances to contract manufacturers, net of current portion	0	[1]	2,222	[1]
Recoverable taxes on purchased property, plant and equipment	15,609	[2]	13,597	[2]
Other	1,979		1,930
Total other assets	$19,725		$20,112

[1]	At December 31, 2012, the amount of $2.2 million relates to the non-current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization was offset against purchases of inventory during 2013.
[2]	At September 30, 2013 and December 31, 2012, the amounts of $15.6 million and $13.6 million, respectively, are recoverable taxes from Brazilian governmental entities.

Balance_Sheet_Components_Accru

Balance Sheet Components Accrued and Other Current Liabilities (Details) (USD $)	Sep. 30, 2013		Dec. 31, 2012
In Thousands, unless otherwise specified	Sep. 30, 2013		Dec. 31, 2012
Balance Sheet Components [Abstract]	'		'
Professional services	$2,859		$824
Accrued vacation	2,179		2,673
Payroll and related expenses	5,099		5,809
Tax-related liabilities	641		851
Deferred rent, current portion	1,111		1,448
Accrued interest	1,435	[1]	965	[1]
Contractual obligations to contract manufacturers, current	5,868		9,952
Customer advances	372		970
Other	741		918
Total accrued and other current liabilities	$20,305		$24,410

[1]	Certain reclassifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Balance_Sheet_Components_Other1

Balance Sheet Components Other Liabilities (Details) (USD $)	Sep. 30, 2013		Dec. 31, 2012
In Thousands, unless otherwise specified	Sep. 30, 2013		Dec. 31, 2012
Balance Sheet Components [Abstract]	'		'
Contractual obligations to contract manufacturers, non-current	$1,000		$4,000
Fair market value of swap obligations	3,074		1,367
Fair value of compound embedded derivative liability(1)	13,836	[1]	7,894	[1]
Tax-related liabilities(2)	469	[2]	1,609	[2]
Other(2)	1,025	[2]	1,063	[2]
Total other liabilities	$19,404		$15,933

[1]	The compound embedded derivative liability represents the fair value of the equity conversion feature and a "make-whole" feature related to the outstanding senior unsecured convertible promissory notes issued to Total.
[2]	Certain reclassifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Commitments_and_Contingencies_1

Commitments and Contingencies (Details) (USD $)	3 Months Ended		9 Months Ended
Commitments and Contingencies (Details) (USD $)	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012	Dec. 31, 2012
Commitments and Contingencies Disclosure [Abstract]	'	'	'	'	'
Operating Leases, Rent Expense	$1,400,000	$1,200,000	$3,500,000	$3,700,000	'
Capital Leases, Future Minimum Payments Due [Abstract]	'	'	'	'	'
2013 (Six Months)	274,000	'	274,000	'	'
2014	1,007,000	'	1,007,000	'	'
2015	289,000	'	289,000	'	'
2016	0	'	0	'	'
2017	0	'	0	'	'
Thereafter	0	'	0	'	'
Total future minimum lease payments	1,570,000	'	1,570,000	'	'
Less: amount representing interest	-75,000	'	-75,000	'	'
Present value of minimum lease payments	1,495,000	'	1,495,000	'	'
Less: current portion	-1,031,000	'	-1,031,000	'	-1,366,000
Long-term portion	464,000	'	464,000	'	1,244,000
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]	'	'	'	'	'
2013 (Six Months)	1,477,000	'	1,477,000	'	'
2014	6,277,000	'	6,277,000	'	'
2015	6,581,000	'	6,581,000	'	'
2016	6,595,000	'	6,595,000	'	'
2017	6,585,000	'	6,585,000	'	'
Thereafter	38,973,000	'	38,973,000	'	'
Total future minimum lease payments	66,488,000	'	66,488,000	'	'
Capital Leases And Operating Leases, Future Minimum Payments Due [Abstract]	'	'	'	'	'
Total Lease Obligations - 2013 (Six Months)	1,751,000	'	1,751,000	'	'
Total Lease Obligations - 2014	7,284,000	'	7,284,000	'	'
Total Lease Obligations - 2015	6,870,000	'	6,870,000	'	'
Total Lease Obligations - 2016	6,595,000	'	6,595,000	'	'
Total Lease Obligations - 2017	6,585,000	'	6,585,000	'	'
Total Lease Obligations - Thereafter	38,973,000	'	38,973,000	'	'
Total Lease Obligations - Total Future minimum leases payments	$68,058,000	'	$68,058,000	'	'

Commitments_and_Contingencies_2

Commitments and Contingencies Guarantor Arrangements/Purchase Obligations and Other Matters (Details)

Sep. 30, 2013

Nov. 30, 2010

Sep. 30, 2013

Nov. 15, 2011

Sep. 30, 2013

Nov. 15, 2011

Sep. 30, 2013

Dec. 31, 2011

Jul. 13, 2012

Sep. 30, 2013

Jul. 13, 2012

Mar. 18, 2013

Sep. 30, 2013

Apr. 30, 2013

USD ($)

FINEP Credit Facility [Member]

Performance Guarantee [Member]

BNDES Credit Facility [Member]

Banco Pine July 2012 Loan Agreement [Member]

Nossa Caixa Loan Agreement [Member]

Pine and Nossa Caixa Loan Agreement [Member]

ABC Brasil Agreement [Member]

Tate & Lyle Termination Agreement [Member]

Loans and Notes Payable [Member]

Chattel Mortgage [Member]

Payment Guarantee [Member]

BNDES [Member]

BRL

USD ($)

BRL

USD ($)

Amendment of Lease Agreement - Emeryville [Member]

BRL

USD ($)

BRL

USD ($)

BRL

USD ($)

disbursement

Loss Contingencies [Line Items]

Lease Incentive, Elimination of Debt, Amount

$1,600,000

Monthly Rent Credit, Current

71,000

Monthly Rent Credit, Noncurrent

42,000

Line of Credit Facility, Maximum Borrowing Capacity

6,400,000

2,900,000

Research and Development Asset Acquired Other than Through Business Combination, Fair Value Acquired

6,000,000

2,700,000

Disbursements Received After Compliance with Certain Terms and Conditions (in disbursements)

Guaranty Liabilities

3,300,000

1,500,000

Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount

11,200,000

24,900,000

30,500,000

68,000,000

Debt Instrument, Face Amount

22,000,000

30,000,000

23,300,000

52,000,000

Export Financing Agreement

2,500,000

Period Required For Restricted Cash

'3 months

Restricted Cash and Cash Equivalents

100,000

200,000

Purchase Obligation

11,800,000

Contractual Obligation

11,100,000

Accrued Loss on Purchase Commitments

4,000,000

Termination Agreement, Payment Amount

6,200,000

8,800,000

Termination Agreement, Outstanding Liability

2,600,000

Termination Agreement, Outstanding Invoice Payment

$3,600,000

Debt_Details

Debt (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified	Sep. 30, 2013	Dec. 31, 2012
Debt Instrument [Line Items]	'	'
Total debt	$118,838	$104,164
Less: current portion	-5,448	-3,325
Long-term debt	113,390	100,839
Convertible Debt [Member]	'	'
Debt Instrument [Line Items]	'	'
Total debt	25,000	25,000
Years ending December 31: [Abstract]	'	'
2013 (Six Months)	192	'
2014	760	'
2015	765	'
2016	761	'
2017	25,125	'
Thereafter	0	'
Total future minimum payments	27,603	'
Less: amount representing interest	-2,603	'
Present value of minimum debt payments	25,000	'
Less: current portion	0	'
Noncurrent portion of debt	25,000	'
Related Party Convertible Notes [Member]	'	'
Debt Instrument [Line Items]	'	'
Total debt	58,091	39,033
Years ending December 31: [Abstract]	'	'
2013 (Six Months)	0	'
2014	0	'
2015	0	'
2016	0	'
2017	83,267	'
Thereafter	0	'
Total future minimum payments	83,267	'
Less: amount representing interest	-25,176	'
Present value of minimum debt payments	58,091	'
Less: current portion	0	'
Noncurrent portion of debt	58,091	'
Notes Payable [Member]	'	'
Debt Instrument [Line Items]	'	'
Total debt	0	1,572
Loans Payable [Member]	'	'
Debt Instrument [Line Items]	'	'
Total debt	25,997	26,150
Years ending December 31: [Abstract]	'	'
2013 (Six Months)	492	'
2014	5,243	'
2015	4,042	'
2016	3,887	'
2017	3,726	'
Thereafter	15,052	'
Total future minimum payments	32,442	'
Less: amount representing interest	-6,445	'
Present value of minimum debt payments	25,997	'
Less: current portion	-3,286	'
Noncurrent portion of debt	22,711	'
Credit Facility [Member]	'	'
Debt Instrument [Line Items]	'	'
Total debt	9,750	12,409
Years ending December 31: [Abstract]	'	'
2013 (Six Months)	682	'
2014	2,681	'
2015	2,542	'
2016	2,404	'
2017	2,264	'
Thereafter	579	'
Total future minimum payments	11,152	'
Less: amount representing interest	-1,402	'
Present value of minimum debt payments	9,750	'
Less: current portion	-2,162	'
Noncurrent portion of debt	$7,588	'

Debt_FINEP_Credit_Facility_Det

Debt FINEP Credit Facility (Details)	0 Months Ended
In Millions, unless otherwise specified	Nov. 30, 2010	Sep. 30, 2013	Sep. 30, 2013	Dec. 31, 2012	Dec. 31, 2012	Nov. 30, 2010	Nov. 30, 2010	Dec. 31, 2012	Nov. 30, 2010
	FINEP Credit Facility [Member]	Chattel Mortgage [Member]	Chattel Mortgage [Member]	Chattel Mortgage [Member]	Chattel Mortgage [Member]	Chattel Mortgage [Member]	Minimum [Member]	FINEP Project [Member]	FINEP Project [Member]
	Monthly_installment	FINEP Credit Facility [Member]	FINEP Credit Facility [Member]	FINEP Credit Facility [Member]	FINEP Credit Facility [Member]	FINEP Credit Facility [Member]	FINEP Credit Facility [Member]	USD ($)	BRL
		USD ($)	BRL	USD ($)	BRL	BRL
Line of Credit Facility [Line Items]	'	'	'	'	'	'	'	'	'
Line of Credit Facility, Maximum Borrowing Capacity	'	$2.90	'	'	'	6.4	'	'	'
Debt Instrument, Interest Rate, Stated Percentage	5.00%	'	'	'	'	'	'	'	'
Long-term Debt, Percentage Bearing Fixed Interest, Percentage Rate	'	'	'	'	'	'	6.00%	'	'
Debt Instrument, Basis Spread on Variable Rate	5.00%	'	'	'	'	'	'	'	'
Long-term Debt, Percentage Bearing Variable Interest, Percentage Rate	11.00%	'	'	'	'	'	'	'	'
Debt Instrument Debt Default Fine Percentage	10.00%	'	'	'	'	'	'	'	'
Debt Instrument Interest On Late Balance Percentage Per Month	1.00%	'	'	'	'	'	'	'	'
Line of Credit Facility Number of Monthly Payments (in monthly installment)	81	'	'	'	'	'	'	'	'
Line of Credit Facility, Amount Outstanding	'	2.5	5.5	3.1	6.4	'	'	'	'
Research and Development Project, Amount To Be Contributed From Company Funds	'	'	'	'	'	'	'	6.5	14.5
Research and Development Project Amount To Be Contributed From Company Prior To Release Of Second Tranche	'	'	'	'	'	'	'	'	11.1
Guaranty Liabilities	'	$1.50	'	'	'	3.3	'	'	'
Period Of Time Amounts Released Must Be Used	'30 months	'	'	'	'	'	'	'	'

Debt_BNDES_Credit_Facility_Det

Debt BNDES Credit Facility (Details) (BNDES Credit Facility [Member], BNDES [Member])	1 Months Ended					1 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2011	Sep. 30, 2013	Sep. 30, 2013	Dec. 31, 2012	Dec. 31, 2012	Dec. 31, 2011	Sep. 30, 2013
	BRL	USD ($)	BRL	USD ($)	BRL	Maximum [Member]	Maximum [Member]
	Monthly_installment					BRL	USD ($)
Line of Credit Facility [Line Items]	'	'	'	'	'	'	'
Line of Credit Facility, Maximum Borrowing Capacity	'	'	'	'	'	22.4	$10
Line of Credit Facility, Initial Tranche	'	'	'	'	'	19.1	8.6
Line of Credit Facility, Additional Tranche, Available Upon Delivery of Additional Guarantees	'	'	'	'	'	3.3	1.5
Period Credit Line Is Available	'	'	'	'	'	'12 months	'
Line of Credit Facility Number of Monthly Payments (in monthly installment)	60	'	'	'	'	'	'
Debt Instrument, Interest Rate, Stated Percentage	7.00%	'	'	'	'	'	'
Line of Credit Facility, Unused Capacity, Commitment Fee Percentage	0.10%	'	'	'	'	'	'
Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount	24.9	11.2	'	'	'	'	'
Line of Credit Facility, Bank Guarantee, Percentage	10.00%	'	'	'	'	'	'
Line of Credit Facility, Second Tranche Floor	19.1	'	'	'	'	'	'
Line of Credit Facility, Bank Guarantee, Percentage, Second Tranche	90.00%	'	'	'	'	'	'
Guarantor Obligations, Liquidation Proceeds, Percentage	130.00%	'	'	'	'	'	'
Line of Credit Facility, Amount Outstanding	'	$7.30	16.2	$9.30	19.1	'	'

Debt_Notes_Payable_Details

Debt Notes Payable (Details) (Notes Payable, Other Payables-Lessor [Member], USD $)	Sep. 30, 2013	Dec. 31, 2012	Oct. 31, 2008	Oct. 31, 2008	Oct. 31, 2008	Apr. 30, 2013
	Sep. 30, 2013	Dec. 31, 2012	Oct. 31, 2008	Minimum [Member]	Maximum [Member]	Amendment of Lease Agreement - Emeryville [Member]
Debt Instrument [Line Items]	'	'	'	'	'	'
Debt Instrument, Face Amount	'	'	$3,300,000	'	'	'
Debt Instrument, Interest Rate, Stated Percentage	'	'	9.50%	'	'	'
Repayment Period	'	'	'	'55 months	'120 months	'
Notes payable outstanding	0	1,600,000	'	'	'	'
Lease Incentive, Elimination of Debt, Amount	'	'	'	'	'	$1,400,000

Debt_Convertible_Notes_Details

Debt Convertible Notes (Details) (USD $)

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Jul. 30, 2012

Sep. 30, 2013

Dec. 31, 2012

Feb. 29, 2012

Dec. 02, 2013

Oct. 31, 2013

Jul. 31, 2013

Jun. 30, 2013

Jul. 30, 2012

Jul. 31, 2014

Jul. 30, 2012

Jul. 31, 2014

Unsecured Senior Convertible Promissory Notes [Member]

Convertible Debt [Member]

Fidelity [Member]

Subsequent Event [Member]

Temasek Bridge Note [Member]

Initial Installment [Member]

Second Installment [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Subsequent Event [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Subsequent Event [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Subsequent Event [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Debt Instrument [Line Items]

Debt Instrument, Face Amount

$105,000,000

$25,000,000

$20,000,000

$10,000,000

$30,000,000

$21,700,000

$10,850,000

Debt Instrument, Interest Rate, Stated Percentage

1.50%

3.00%

5.50%

Debt Instrument, Convertible, Conversion Price

$7.07

$2.20

$3.08

Debt Instrument, Convertible, Common Stock, Shares

3,536,968.39

Percentage of Principal Amount of Notes, Required to Be Repaid In An Acquisition

101.00%

Debt Instrument, Debt Covenant, Outstanding Debt, Maximum

200,000,000

Debt Instrument, Debt Covenant, Percentage of Consolidated Total Assets, Maximum

50.00%

Debt Instrument, Debt Covenant, Outstanding Secured Debt, Maximum

125,000,000

Debt Instrument, Debt Covenant, Secured Debt, Percentage of Consolidated Total Assets, Maximum

30.00%

Bridge Loan

35,000,000

Long-term Debt

$118,838,000

$104,164,000

$25,000,000

Debt_Related_Party_Convertible

Debt Related Party Convertible Notes (Details) (USD $)

Sep. 30, 2013

Dec. 31, 2012

Aug. 31, 2013

Jul. 30, 2012

Sep. 30, 2013

Dec. 24, 2012

Jul. 30, 2012

Sep. 14, 2012

Jul. 30, 2012

Jul. 31, 2013

Jul. 26, 2013

Jun. 30, 2013

Jun. 06, 2013

Sep. 30, 2013

Dec. 31, 2012

Dec. 24, 2012

Jul. 31, 2013

Jun. 30, 2013

Jul. 30, 2012

Aug. 31, 2013

Oct. 31, 2013

Dec. 02, 2013

Jul. 31, 2014

Oct. 31, 2013

Mar. 24, 2013

Aug. 31, 2013

August 2013 Convertible Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Related Party Convertible Notes [Member]

Private Placement [Member]

Initial Installment [Member]

Second Installment [Member]

Select Whichever Greater At Consideration [Member]

First Tranche [Member]

Second Tranche [Member]

Subsequent Event [Member]

May 15th 2013 [Member]

June 15th 2013 [Member]

Common Stock [Member]

Unsecured Senior Convertible Notes 1.5% Due 2017 [Member]

July 2013 Convertible Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

August 2013 Convertible Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Initial Installment [Member]

Second Installment [Member]

First Tranche [Member]

Second Tranche [Member]

Subsequent Event [Member]

Unsecured Senior Convertible Promissory Notes [Member]

August 2013 Convertible Notes [Member]

Debt Instrument [Line Items]

Debt Instrument, Amended Promissory Note, Amount

$14,600,000

$9,200,000

$5,400,000

Debt Instrument, Face Amount

105,000,000

38,300,000

15,000,000

20,000,000

10,000,000

20,000,000

10,000,000

30,000,000

42,600,000

30,400,000

21,700,000

10,850,000

Debt Instrument, Interest Rate, Stated Percentage

1.50%

Proceeds from Convertible Debt

15,000,000

Debt Conversion, Converted Instrument, Amount

23,300,000

Debt Instrument, Convertible, Common Stock, Shares

1,677,852

Future Proceeds from Convertible Debt

60,000,000

30,000,000

35,000,000

25,000,000

Future Cancellation Of Debt, Amount

13,000,000

7,600,000

5,400,000

44,200,000

7,600,000

Class of Warrant or Right, Number of Securities Called by Warrants or Rights

1,000,000

Class of Warrant or Right, Exercise Price of Warrants or Rights

0.01

Debt Instrument, Convertible, Conversion Price

$7.07

$3.08

$2.98

$3.08

$2.20

$2.44

$2.87

Collaboration Agreement, Funding Obligation Advanced Installments

10,000,000

Debt Instrument, Closing Price Plus Incremental Rate

$0.01

Debt Instrument, Interest Rate, Default Rate, Stated Percentage

2.50%

Debt Instrument, Convertible, Period Prior to Maturity to Eligible For Conversion

'10 days

Period of Lock-up Upon Conversion of Debt

'6 months

Convertible Debt, Amount Outstanding

53,300,000

Debt Instrument, Early Repayment, Percentage of Principal

101.00%

Debt Instrument, Debt Covenant, Outstanding Debt, Maximum

200,000,000

Debt Instrument, Debt Covenant, Percentage of Consolidated Total Assets, Maximum

50.00%

Debt Instrument, Debt Covenant, Outstanding Secured Debt, Maximum

125,000,000

Debt Instrument, Debt Covenant, Secured Debt, Percentage of Consolidated Total Assets, Maximum

30.00%

Long-term Debt

118,838,000

104,164,000

58,091,000

39,033,000

Debt Instrument, Unamortized Discount

20,200,000

9,300,000

Termination Agreement, Additional Owed Payment

$30,400,000

Debt_Loans_Payable_Details

Debt Loans Payable (Details)

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2012

Sep. 30, 2013

Jul. 13, 2012

Sep. 30, 2013

Dec. 31, 2012

Oct. 31, 2012

Sep. 30, 2013

Dec. 31, 2012

Dec. 31, 2009

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Sep. 30, 2012

Apr. 30, 2013

Mar. 31, 2013

Mar. 18, 2013

Sep. 30, 2013

USD ($)

Banco Pine S.A Loan Agreement June 2012 [Member]

Pine and Nossa Caixa Loan Agreement [Member]

Banco Pine July 2012 Loan Agreement [Member]

Nossa Caixa Loan Agreement [Member]

Loans Payable [Member]

Loans Payable Lessor Emeryville Plant [Member]

Interest Rate Swap [Member]

Amendment of Lease Agreement - Emeryville [Member]

ABC Brasil Agreement [Member]

Bridge Loan [Member]

USD ($)

BRL

USD ($)

Pine and Nossa Caixa Loan Agreement [Member]

USD ($)

Banco Pine July 2012 Loan Agreement [Member]

Loans Payable [Member]

USD ($)

Loans Payable [Member]

USD ($)

BRL

Monthly_installment

USD ($)

BRL

USD ($)

Debt Instrument [Line Items]

Debt Instrument, Face Amount

$25,600,000

52,000,000

$23,300,000

52,000,000

22,000,000

30,000,000

$600,000

$300,000

Debt Instrument, Interest Rate, Stated Percentage

5.50%

3.24%

10.00%

Days of Interruption of Manufacturing Activities at Plant

'30 days

Repayment Period

'96 months

Long-term Debt

118,838,000

104,164,000

25,997,000

26,150,000

23,300,000

25,400,000

200,000

2,500,000

Lease Incentive, Elimination of Debt, Amount

200,000

Debt Instrument, Interest Rate, Monthly Stated Percentage

0.45%

Notional Amount of Interest Rate Derivatives

9,900,000

22,000,000

Derivative, Fixed Interest Rate

3.94%

Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount

30,500,000

68,000,000

Debt Instrument, Period of Interest Only Quarterly Payments

'2 years

Number Of Equal Monthly Installments

Loans Payable to Bank

400,000

Export Financing Agreement

2,500,000

Debt Instrument, Term

'1 year

Debt Instrument, Debt Discount Related Party

($20,200,000)

Debt_Letters_of_Credit_Details

Debt Letters of Credit (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012	Sep. 30, 2012
Debt Disclosure [Abstract]	'	'	'
Letters of Credit Outstanding, Amount	'	'	$1,000,000
Restricted cash	$956,000	$955,000	'

Joint_Ventures_and_Noncontroll2

Joint Ventures and Noncontrolling Interest Narrative (Details)

3 Months Ended

9 Months Ended

0 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Mar. 26, 2013

Jun. 30, 2011

Mar. 26, 2013

Apr. 14, 2010

Sep. 30, 2013

Mar. 26, 2013

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

USD ($)

Joint Venture with Cosan [Member]

Novvi LLC [Member]

SMA Industria Quimica S.A. [Member]

Maximum [Member]

Granting IP License to Novvi [Member]

Novvi LLC [Member]

Revenue from Research and Devolopment [Member]

Sales Revenue, Goods, Net [Member]

USD ($)

Corporate Joint Venture [Member]

Amyris Brasil S.A. Subsidiary [Member]

Corporate Joint Venture [Member]

SMA Industria Quimica S.A. [Member]

Joint Venture with Cosan [Member]

USD ($)

Novvi LLC [Member]

BRL

member

Corporate Joint Venture [Member]

USD ($)

BRL

Redeemable Noncontrolling Interest [Line Items]

Initial Term of Joint Venture

'20 years

Equity Method Investment Number of Members of Executive Committee

Equity Method Investment Number of Company Appointed Members of Executive Committee

Equity Method Investment Number of Members of Executive Committee that are Senior Executive

Equity Method Investment Number of Members of Board of Directors

Equity Method Investment Number of Members of Board of Directors Appointed by Each Venture

Due from Joint Ventures

$27,700,000

61,800,000

Equity Method Investment Period Company is required to Purchase Output of SMA

Equity Method Investment, Ownership Percentage

50.00%

Initial Term of Shareholders' Agreement

Equity Method Investment Ownership Percentage Required

10.00%

Obligation to Fund Agreement, Cash Portion

10,000,000

Funding Obligation, in Kind

10,000,000

Initial Contribution to Fund Agreement, Cost Basis

Equity Method Investment, Difference Between Carrying Amount and Underlying Equity

Net loss

-24,228,000

-20,388,000

-95,457,000

-162,419,000

Agreement to Sell Equity Method Investment, Ownership Percentage

50.00%

Agreement to Sell Equity Ownership

22,000

Revenue from Related Parties

$1,000,000

$1,100,000

$2,600,000

$1,000,000

$1,100,000

Joint_Ventures_and_Noncontroll3

Joint Ventures and Noncontrolling Interest Variable Interest Entity (Details) (USD $)	9 Months Ended		1 Months Ended
	Sep. 30, 2013	Mar. 31, 2012	Jan. 31, 2011	Jan. 31, 2011	Sep. 30, 2013
	Variable Interest Entity, Primary Beneficiary [Member]	Variable Interest Entity, Primary Beneficiary [Member]	Glycotech Agreement [Member]	Glycotech Agreement [Member]	Glycotech Agreement [Member]
	consolidated_VIE			Variable Interest Entity, Primary Beneficiary [Member]	Variable Interest Entity, Primary Beneficiary [Member]
Variable Interest Entity [Line Items]	'	'	'	'	'
Period of Initial Term of Collaboration Agreement	'	'	'2 years	'	'
Additional Year Periods of Collaboration Agreement	'	'	'1 year	'	'
Variable Interest Entity, Financial or other support	'	'	'	100.00%	'
Variable Interest Entity Number of Entities (in VIEs)	2	'	'	'	'
Variable Interest Entity, Consolidated, Carrying Amount, Property and Equipment	$22,700,000	'	'	'	'
Variable Interest Entity, Consolidated, Carrying Amount, Other Assets	4,100,000	'	'	'	'
Variable Interest Entity, Consolidated, Carrying Amount, Current Assets	400,000	'	'	'	'
Variable Interest Entity, Consolidated, Carrying Amount, Accounts Payable And Accrued Liabilities	200,000	'	'	'	'
Variable Interest Entity, Consolidated, Carrying Amount, Loan Obligations	'	'	'	'	100,000
Assets	27,118,000	29,564,000	'	'	'
Liabilities	$335,000	$355,000	'	'	'

Joint_Ventures_and_Noncontroll4

Joint Ventures and Noncontrolling Interest Noncontrolling Interest (Details) (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Stockholders' Equity Attributable to Noncontrolling Interest [Roll Forward]	'	'	'	'
Beginning Balance	'	'	($877)	'
Foreign currency translation adjustment,	'	'	-4,099	'
Loss attributable to noncontrolling interest	29	95	-232	772
Ending Balance	-590	'	-590	'
Noncontrolling Interest [Member]	'	'	'	'
Stockholders' Equity Attributable to Noncontrolling Interest [Roll Forward]	'	'	'	'
Beginning Balance	'	'	-877	-240
Foreign currency translation adjustment,	'	'	55	209
Loss attributable to noncontrolling interest	'	'	232	-772
Ending Balance	($590)	($803)	($590)	($803)

Significant_Agreements_Narrati

Significant Agreements (Narrative) (Details) (USD $)

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

0 Months Ended

3 Months Ended

9 Months Ended

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Dec. 31, 2012

Sep. 30, 2013

Apr. 23, 2013

Mar. 13, 2013

Sep. 30, 2013

Mar. 13, 2013

Tate & Lyle Termination Agreement [Member]

International Flavors & Fragrances Inc Agreement [Member]

Firmenich SA Agreement [Member]

Before Firmenich Receives 15 Million Dollars More Than The Company in Agregate [Member]

After Firmenich Received 15 Million Dollars More Than The Company in Agregate [Member]

Firmenich [Member]

payment

Firmenich SA Agreement [Member]

Before Firmenich Receives 15 Million Dollars More Than The Company in Agregate [Member]

After Firmenich Received 15 Million Dollars More Than The Company in Agregate [Member]

Firmenich SA Agreement [Member]

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Termination Agreement, Number of Payments Due

Termination Agreement, Payment Amount

$6,200,000

$8,800,000

Termination Agreement, Outstanding Invoice Payment

3,600,000

Termination Agreement, Additional Owed Payment

5,200,000

Termination Agreement, Outstanding Liability

2,600,000

Loss on purchase commitments and write off of production assets

1,438,000

8,423,000

38,090,000

8,400,000

Production Assets Written Off

6,700,000

Loss Related to Adverse Purchase Commitments

-1,000,000

Deposits Assets, Noncurrent

[1]

2,222,000

[1]

2,700,000

Collaboration Agreement, Range of Funding, First Phase of Collaboration

6,000,000

Collaboration Agreement, Annual Funding

10,000,000

Collaboration Agreement, Annual Funding Period

'3 years

Collaboration Agreement, Initial Payment

10,000,000

Collaboration Agreement, Initial Payment, Recognized as Revenue

2,500,000

5,400,000

Revenue Recognition, Milestone Method, Potential Revenue to be Recognized

5,000,000

Collaboration Agreement, Percentage Shares of Product Margins from Sales of Each Compound

30.00%

50.00%

70.00%

50.00%

Collaboration Agreement, Shares of Product Margins from Sales of Each Compound Threshold Amount Until New Percentage Share Distribution

15,000,000

Collaborator Agreement Performance Bonus

$2,500,000

Collaborator Agreement Performance Bonus, Number of Payment

Collaboration Agreement, No Research and Development Commitments on Either Party Thereafter

'6 years

Collaboration Agreement, Option to Mutually Agree for Additional Research and Development Commitments Thereafter Period of Agreement

'6 years

[1]

At December 31, 2012, the amount of $2.2 million relates to the non-current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization was offset against purchases of inventory during 2013.

Goodwill_and_Intangible_Assets2

Goodwill and Intangible Assets (Details) (USD $)	3 Months Ended		9 Months Ended			9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012	Dec. 31, 2012	Sep. 30, 2013	Dec. 31, 2012	Sep. 30, 2013	Dec. 31, 2012	Oct. 06, 2011
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012	Dec. 31, 2012	Acquired Licenses and Permits [Member]	Acquired Licenses and Permits [Member]	In Process Research and Development [Member]	In Process Research and Development [Member]	Draths Corporation [Member]
Schedule of Finite-Lived and Indefinite-Lived Intangible Assets [Line Items]	'	'	'	'	'	'	'	'	'	'
Indefinite-Lived Intangible Assets (Excluding Goodwill)	'	'	'	'	'	'	'	$8,560	$8,560	$8,600
Finite-Lived Intangible Asset, Useful Life	'	'	'	'	'	'2 years	'	'	'	'
Finite-Lived Intangible Assets, Gross	'	'	'	'	'	772	772	'	'	'
Finite-Lived Intangible Assets, Accumulated Amortization	-772	'	-772	'	-740	-772	-740	'	'	'
Finite-Lived Intangible Assets, Net	'	'	'	'	'	0	32	'	'	'
Goodwill	560	'	560	'	560	'	'	'	'	600
Goodwill and Intangible Assets, Gross	9,892	'	9,892	'	9,892	'	'	'	'	'
Amortization of Intangible Assets	0	-100	-32	-300	'	-32	'	'	'	'
Goodwill and Intangible Assets, Net	$9,120	'	$9,120	'	$9,152	'	'	'	'	'

Stockholders_Equity_Details

Stockholders' Equity (Details) (USD $)

9 Months Ended

0 Months Ended

1 Months Ended

0 Months Ended

Sep. 30, 2013

Sep. 30, 2012

Dec. 31, 2012

Mar. 27, 2013

Jan. 11, 2013

Dec. 24, 2012

Feb. 29, 2012

Dec. 24, 2012

31-May-12

Feb. 29, 2012

Dec. 24, 2012

Jan. 23, 2013

Private Placement [Member]

Convertible Notes Payable [Member]

Commitment Fulfilled [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Equity Incentive Plan, 2010 [Member]

Employee Stock Purchase Plan, 2010 [Member]

Common Stock [Member]

Private Placement [Member]

Class of Stock [Line Items]

Stock Issued During Period, Shares, New Issues

1,533,742

5,033,557

14,177,849

1,736,100

10,160,325

Stock Issued During Period, Price Per Share, New Issues

$3.26

$2.98

$2.36

$5.78

Stock Issued During Period, Value, New Issues

$19,979,000

$4,100,000

$58,700,000

Commitment to purchase company common stock

15,000,000

10,000,000

Proceeds from Issuance of Private Placement

19,981,000

62,490,000

5,000,000

37,200,000

Extinguishment of Debt, Amount

5,000,000

Extinguishment of Debt, Common Stock, Shares

1,677,852

Proceeds from Issuance of Private Placement, First Payment Received

22,200,000

Proceeds from Private Placement Remaining Balance Settled

$15,000,000

Share-based Compensation Arrangement by Share-based Payment Award, Number of Additional Shares Authorized

3,435,483

687,096

Share-based Compensation Arrangement by Share-based Payment Award, Number of Additional Shares Authorized, Percentage Increase of Common Stock, Shares, Outstanding

5.00%

1.00%

Common Stock, Shares, Outstanding

76,245,375

68,709,660

StockBased_Compensation_Plans_1

Stock-Based Compensation Plans - Stock Option Activity (Details) (USD $)

3 Months Ended

9 Months Ended

1 Months Ended

9 Months Ended

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Dec. 31, 2012

Sep. 30, 2013

Stock Options [Member]

$0.10â€”$2.76

$2.79â€”$2.85

$2.87â€”$2.87

$2.89â€”$3.12

$3.23â€”$3.83

$3.86â€”$3.86

$3.93â€”$4.06

$4.31â€”$14.28

$16.00â€”$19.61

$20.41â€”$30.17

$0.10â€”$30.17

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Lower Range Limit

$0.10

$2.79

$2.87

$2.89

$3.23

$3.86

$3.93

$4.31

$16

$20.41

$0.10

Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Upper Range Limit

$2.76

$2.85

$2.87

$3.12

$3.83

$3.86

$4.06

$14.28

$19.61

$30.17

Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]

Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Beginning Balance

8,946,592

Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Net of Forfeitures

2,772,130

Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercises in Period

-193,166

Share-based Compensation Arrangement by Share-based Payment Award, Options, Forfeitures in Period

-2,389,042

Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance

8,946,592

9,136,514

1,218,972

964,895

917,000

918,271

189,639

1,045,052

992,731

919,609

942,063

1,028,282

9,136,514

Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price [Roll Forward]

Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Beginning Balance

$9.07

Share-based Compensation Arrangements by Share-based Payment Award, Options, Grants in Period, Weighted Average Exercise Price

$2.83

Share-based Compensation Arrangements by Share-based Payment Award, Options, Exercises in Period, Weighted Average Exercise Price

$0.87

Share-based Compensation Arrangements by Share-based Payment Award, Options, Forfeitures in Period, Weighted Average Exercise Price

$9.56

Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance

$9.07

$7.23

$2.63

$2.79

$2.87

$2.99

$3.31

$3.86

$3.95

$6.80

$16.31

$23.86

$7.23

Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term

'7 years 5 months 16 days

'7 years 8 months 19 days

'8 years 4 months 2 days

'9 years 9 months

'9 years 8 months 1 day

'9 years 1 month 21 days

'8 years 9 months 15 days

'8 years 1 month 28 days

'4 years 3 months

'6 years 1 month 10 days

'7 years 0 months 18 days

'6 years 10 months 2 days

'7 years 8 months 19 days

Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Intrinsic Value

$954,000

$71,000

Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest, Outstanding, Number

8,454,008

Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest, Outstanding, Weighted Average Exercise Price

$7.44

Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest, Outstanding, Weighted Average Remaining Contractual Term

'7 years 7 months 10 days

Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest, Outstanding, Aggregate Intrinsic Value

71,000

Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number

3,950,398

248,047

204,297

86,438

416,769

926,064

748,254

600,610

719,851

3,950,398

Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price

$9.70

$2.31

$2.85

$3.04

$3.39

$3.86

$3.94

$6.38

$16.29

$23.62

$9.70

Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Remaining Contractual Term

'6 years 2 months 5 days

Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Intrinsic Value

71,000

Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercises in Period, Total Intrinsic Value

$100,000

$2,000,000

$400,000

$2,700,000

StockBased_Compensation_Plans_2

Stock-Based Compensation Plans - Restricted Stock Units and Restricted Stock Activity (Details) (Restricted Stock Units (RSUs) [Member], USD $)	9 Months Ended	12 Months Ended
	Sep. 30, 2013	Dec. 31, 2012
Restricted Stock Units (RSUs) [Member]	'	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]	'	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number	2,550,799	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period	1,100,000	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Vested in Period	-654,619	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Forfeited in Period	-360,995	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number	2,635,185	2,550,799
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Roll Forward]	'	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value	$7.92	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period, Weighted Average Grant Date Fair Value	$2.84	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Vested in Period, Weighted Average Grant Date Fair Value	$5.91	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Forfeited in Period, Weighted Average Grant Date Fair Value	$3.92	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value	$4.20	$7.92
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Outstanding, Weighted Average Remaining Contractual Term	'1 year 0 months 18 days	'1 year 3 months 18 days
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Outstanding, Weighted Average Remaining Contractual Term	'1 year 0 months 18 days	'1 year 3 months 18 days
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Expected to Vest	2,389,722	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Expected to Vest, Weighted Average Grant Date Fair Value	$4.20	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Vested and Expected to Vest , Weighted Average Remaining Contractual Term	'11 months 23 days	'

StockBased_Compensation_Plans_3

Stock-Based Compensation Plans - Stock-Based Compensation Expense (Details) (USD $)	3 Months Ended		9 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Allocated Share-based Compensation Expense	$4,433,000	$5,965,000	$13,611,000	$21,400,000
Research and Development Expense [Member]	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Allocated Share-based Compensation Expense	1,132,000	1,450,000	3,428,000	4,521,000
Sales General and Administrative Expense [Member]	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Allocated Share-based Compensation Expense	3,301,000	4,515,000	10,183,000	16,879,000
Non Employee Share Based Compensation [Member] \| Stock Options [Member]	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Expected dividend yield	0.00%	0.00%	0.00%	0.00%
Risk-free interest rate	1.20%	1.30%	1.40%	1.50%
Expected term (in years)	'4 years	'6 years 10 months 24 days	'5 years 3 months 26 days	'7 years 1 month 6 days
Expected volatility	81.00%	79.00%	82.00%	77.00%
Employee Share Based Compensation [Member]	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Employee Service Share-based Compensation, Nonvested Awards, Total Compensation Cost Not yet Recognized	18,000,000	'	18,000,000	'
Employee Service Share-based Compensation, Nonvested Awards, Total Compensation Cost Not yet Recognized, Period for Recognition	'	'	'2 years 10 months 2 days	'
Expected dividend yield	0.00%	0.00%	0.00%	0.00%
Risk-free interest rate	1.60%	0.90%	1.40%	1.10%
Expected term (in years)	'6 years 1 month 6 days	'5 years 10 months 24 days	'6 years 1 month 6 days	'6 years
Expected volatility	81.00%	79.00%	82.00%	76.00%
Employee Share Based Compensation [Member] \| Restricted Stock Units (RSUs) [Member]	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Employee Service Share-based Compensation, Nonvested Awards, Total Compensation Cost Not yet Recognized	$5,300,000	'	$5,300,000	'
Employee Service Share-based Compensation, Nonvested Awards, Total Compensation Cost Not yet Recognized, Period for Recognition	'	'	'1 year 7 months 2 days	'

Related_Party_Transactions_Det

Related Party Transactions (Details) (USD $)

3 Months Ended

9 Months Ended

0 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

1 Months Ended

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Dec. 31, 2012

Mar. 27, 2013

Jan. 11, 2013

Dec. 24, 2012

Feb. 29, 2012

Dec. 24, 2012

31-May-12

Feb. 29, 2012

Aug. 31, 2013

Sep. 30, 2013

Jul. 30, 2012

Jul. 31, 2013

Jul. 26, 2013

Jun. 30, 2013

Jun. 06, 2013

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Aug. 31, 2013

Oct. 31, 2013

Oct. 16, 2013

Oct. 31, 2013

Private Placement [Member]

August 2013 Convertible Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Novvi LLC [Member]

Revenue from Research and Devolopment [Member]

Maximum [Member]

Subsequent Event [Member]

Cancellation of the Temasek Bridge Note [Member]

Common Stock [Member]

July 2013 Convertible Notes [Member]

Novvi LLC [Member]

August 2013 Convertible Notes [Member]

Temasek Bridge Note [Member]

Maximum [Member]

Subsequent Event [Member]

August 2013 Convertible Notes [Member]

Temasek Bridge Note [Member]

Related Party Transaction [Line Items]

Stock Issued During Period, Shares, New Issues

1,533,742

5,033,557

14,177,849

1,736,100

10,160,325

Stock Issued During Period, Price Per Share, New Issues

$3.26

$2.98

$2.36

$5.78

Stock Issued During Period, Value, New Issues

$19,979,000

$4,100,000

$58,700,000

Beneficial Owner, Ownership Percentage of Common Stock

5.00%

Proceeds from Issuance of Private Placement

19,981,000

62,490,000

5,000,000

37,200,000

Commitment to purchase company common stock

15,000,000

Debt Instrument, Interest Rate, Stated Percentage

1.50%

5.50%

Debt Instrument, Interest Rate, Stated Default Percentage

2.00%

Debt Instrument, Face Amount

105,000,000

20,000,000

10,000,000

73,000,000

51,800,000

Bridge Loan

5,000,000

35,000,000

Future Cancellation Of Debt, Amount

13,000,000

44,200,000

35,000,000

Revenue from Related Parties

1,000,000

1,100,000

2,600,000

Related party accounts receivable

1,022,000

1,100,000

Related party grants and collaborations revenue

$9,775,000

$2,647,000

$9,775,000

Income_Taxes_Narrative_Details

Income Taxes - Narrative (Details)	3 Months Ended		9 Months Ended		3 Months Ended
In Millions, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2013
	USD ($)	USD ($)	USD ($)	USD ($)	Amyris Brasil S.A. Subsidiary [Member]	Amyris Brasil S.A. Subsidiary [Member]
					USD ($)	BRL
Income Tax Contingency [Line Items]	'	'	'	'	'	'
Income Tax Expense (Benefit), Continuing Operations	($1.40)	$0.30	($1)	$0.80	$1.60	'
Debt Instrument, Face Value, Loans Converted to Equity	'	'	'	'	$40.20	89.7

Segment_Information_Details

Segment Information (Details) (USD $)	3 Months Ended			9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013		Sep. 30, 2012	Sep. 30, 2013		Sep. 30, 2012	Dec. 31, 2012
	business_activity			business_activity
	segment_manager			segment_manager
Revenues from External Customers and Long-Lived Assets [Line Items]	'		'	'		'	'
Segment Reporting, Number of Business Activities	1		'	1		'	'
Segment Reporting, Number of Segment Managers Held Accountable	0		'	0		'	'
Revenues	$7,004		$19,108	$25,722		$67,840	'
Long-Lived Assets	140,718		'	140,718		'	163,121
United States [Member]	'		'	'		'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'		'	'		'	'
Revenues	2,037		3,905	12,060		46,807	'
Long-Lived Assets	56,558	[1]	'	56,558	[1]	'	70,085	[1]
Brazil [Member]	'		'	'		'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'		'	'		'	'
Revenues	1,046		1,053	3,123		2,741	'
Long-Lived Assets	82,649	[1]	'	82,649	[1]	'	91,170	[1]
Europe [Member]	'		'	'		'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'		'	'		'	'
Revenues	2,829		12,452	7,059		15,785	'
Long-Lived Assets	1,511		'	1,511		'	1,866
Asia [Member]	'		'	'		'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'		'	'		'	'
Revenues	$1,092		$1,698	$3,480		$2,507	'

[1]	Certain reclassifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not change previously reported consolidated financial statements.

Comprehensive_Income_Loss_Deta

Comprehensive Income (Loss) (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified	Sep. 30, 2013	Dec. 31, 2012
Equity [Abstract]	'	'
Foreign currency translation adjustment, net of tax	($16,961)	($12,807)
Total accumulated other comprehensive loss	($16,961)	($12,807)

Net_Loss_Attributable_to_Commo2

Net Loss Attributable to Common Stockholders and Net Loss per Share (Details) (USD $)	3 Months Ended		9 Months Ended
In Thousands, except Share data, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Net loss attributable to Amyris, Inc. common stockholders (in dollars)	($24,199)	($20,293)	($95,689)	($161,647)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted (in shares)	76,205,853	58,964,226	75,167,877	55,552,949
Net loss per share attributable to common stockholders, basic and diluted (in dollars per share)	($0.32)	($0.34)	($1.27)	($2.91)
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	31,903,437	21,157,472	31,903,437	21,157,472
Stock Options [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	9,136,514	8,345,400	9,136,514	8,345,400
Convertible Notes Payable [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	20,110,650	11,077,785	20,110,650	11,077,785
Common Stock Subject to Repurchase [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	1	301	1	301
Warrant [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	21,087	21,087	21,087	21,087
Restricted Stock [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	2,635,185	1,712,899	2,635,185	1,712,899

Subsequent_Events_Details

Subsequent Events (Details) (USD $)

Sep. 30, 2013

Jul. 30, 2012

Dec. 02, 2013

Oct. 31, 2013

Aug. 31, 2013

Sep. 30, 2013

Oct. 31, 2013

Aug. 31, 2013

Oct. 31, 2013

Aug. 31, 2013

Oct. 31, 2013

Aug. 31, 2013

Oct. 16, 2013

Unsecured Senior Convertible Promissory Notes [Member]

Temasek Bridge Note [Member]

August 2013 Convertible Notes [Member]

First Tranche [Member]

Second Tranche [Member]

First and Second Tranche [Member]

Maximum [Member]

Subsequent Event [Member]

Cancellation of the Temasek Bridge Note [Member]

Subsequent Event [Member]

August 2013 Convertible Notes [Member]

Subsequent Event [Member]

Subsequent Event [Line Items]

Debt Instrument, Convertible Promissory Note, Held by Third Party

$48,300,000

Debt Instrument, Convertible, Conversion Price

$7.07

$2.20

$2.44

$2.87

Debt Instrument, Convertible Conversion, Minimum Period

'18 months

'12 months

Debt Instrument, Convertible, Conversion Price, Event Date Price

$2.15

Plant Manufacturing Production, Volume

1,000,000

Plant Manufacturing Production, Period

'45 days

Plant Manufacturing Production, Product Sales, Percentage

5.00%

Debt Instrument, Convertible, Conversion Price, Milestone Price

$1.87

Debt Instrument, Convertible, Conversion Price, Interest Accrued for Six Months

5.00%

Debt Instrument, Convertible, Conversion Price, Interest Accrued for Three Months

6.50%

13.00%

Debt Instrument, Convertible, Conversion Price, Interest Accrued Thereafter

8.00%

16.00%

Debt Instrument, Convertible, Conversion Price, Interest Period

'30 months

'36 months

Debt Instrument, Convertible, Conversion Price, Interest Accrued

10.00%

Bridge Loan

35,000,000

5,000,000

Future Cancellation Of Debt, Amount

35,000,000

13,000,000

44,200,000

7,600,000

5,400,000

Debt Instrument, Interest Rate, Stated Percentage

1.50%

5.50%

Debt Instrument, Amended Additional Investor Amount

7,600,000

Debt Instrument, Amended Promissory Note, Amount

14,600,000

9,200,000

5,400,000

Debt Instrument, Face Amount

$105,000,000

$42,600,000

$30,400,000

$73,000,000

$51,800,000

Debt Instrument, Term

'60 months

'5 years

Debt Instrument, Convertible, Conversion Price, Interest Accrued for Defaults

6.50%

12.00%

Percentage of Principal Amount of Notes, Required to Be Repaid In Change of Control

101.00%