UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 10-Q

☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

FOR THE QUARTERLY PERIOD ENDED ~~SEPTEMBER 30, 2020~~MARCH 31, 2021

☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

FOR THE TRANSITION PERIOD FROM TO

Commission file number 000-19319

Vertex Pharmaceuticals Incorporated

(Exact name of registrant as specified in its charter)

Massachusetts

(State or other jurisdiction of incorporation or organization)

50 Northern Avenue, Boston, Massachusetts

(Address of principal executive offices)

04-3039129

(I.R.S. Employer Identification No.)

02210

(Zip Code)

Registrant’s telephone number, including area code (617) 341-6100

Securities registered pursuant to Section 12(b) of the Act:

Title of each class

Trading Symbol

Name of each exchange on which registered

Common Stock, $0.01 Par Value Per Share

VRTX

The Nasdaq Global Select Market

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☒ No ☐

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ☒ No ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

Large accelerated filer ☒ Accelerated filer ☐ Non-accelerated filer ☐ Smaller reporting company ☐ Emerging growth company ☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ☒

Indicate the number of shares outstanding of each of the issuer’s classes of common stock, as of the latest practicable date.


Common Stock, par value $0.01 per share			~~260,037,894~~258,865,671			Outstanding at ~~October 23, 2020~~April 22, 2021

Table of Contents

VERTEX PHARMACEUTICALS INCORPORATED

FORM 10-Q

FOR THE QUARTER ENDED ~~SEPTEMBER 30, 2020~~MARCH 31, 2021

TABLE OF CONTENTS


		Page
Part I. Financial Information
Item 1.	Financial Statements	2
	Condensed Consolidated Financial Statements (unaudited)	2
	Condensed Consolidated Statements of Operations - Three ~~and Nine~~ Months Ended ~~September 30,~~March 31, 2021 and 2020 ~~and 2019~~	2
	Condensed Consolidated Statements of Comprehensive Income - Three ~~and Nine~~ Months Ended ~~September 30,~~March 31, 2021 and 2020 ~~and 2019~~	3
	Condensed Consolidated Balance Sheets - ~~September 30, 2020~~March 31, 2021 and December 31, ~~2019~~2020	4
	Condensed Consolidated Statements of Shareholders' Equity - Three ~~and Nine~~ Months Ended ~~September 30,~~March 31, 2021 and 2020 ~~and 2019~~	5
	Condensed Consolidated Statements of Cash Flows - Three ~~and Nine~~ Months Ended ~~September 30,~~March 31, 2021 and 2020 ~~and 2019~~	6
	Notes to Condensed Consolidated Financial Statements	7
Item 2.	Management's Discussion and Analysis of Financial Condition and Results of Operations	2422
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	3733
Item 4.	Controls and Procedures	3833
Part II. Other Information
Item 1.	Legal Proceedings	3833
Item 1A.	Risk Factors	3934
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	4135
Item 5.	Other Information	35
Item 6.	Exhibits	4136
Signatures		4237

“We,” “us,” “Vertex” and the “Company” as used in this Quarterly Report on Form 10-Q refer to Vertex Pharmaceuticals Incorporated, a Massachusetts corporation, and its subsidiaries.

“Vertex,” “KALYDECO®,” “ORKAMBI®,” “SYMDEKO®,” “SYMKEVI®” and “TRIKAFTA®” are registered trademarks of Vertex. The trademark for “KAFTRIOTM” is pending in the United States and registered in the European Union. Other brands, names and trademarks contained in this Quarterly Report on Form 10-Q are the property of their respective owners.

We use the brand name for our products when we refer to the product that has been approved and with respect to the indications on the approved label. Otherwise, including in discussions of our cystic fibrosis development programs, we refer to our compounds by their scientific (or generic) name or VX developmental designation.

Table of Contents

Part I. Financial Information

Item 1. Financial Statements

VERTEX PHARMACEUTICALS INCORPORATED

Condensed Consolidated Statements of Operations

(unaudited)

(in thousands, except per share amounts)


		Three Months Ended September 30,				Nine Months Ended September 30,					Three Months Ended March 31,
		2020		2019		2020		2019				2021		2020
Revenues:	Revenues:									Revenues:
Product revenues, net	Product revenues, net	$	1,536,271	$	949,828	$	4,575,863	$	2,747,461	Product revenues, net		$	1,723,305	$	1,515,107
Collaborative and royalty revenues		2,000		0		2,000		2,095
Other revenues										Other revenues		1,000		0
Total revenues	Total revenues	1,538,271		949,828		4,577,863		2,749,556		Total revenues		1,724,305		1,515,107
Costs and expenses:	Costs and expenses:									Costs and expenses:
Cost of sales	Cost of sales	186,182		131,914		533,199		362,746		Cost of sales		192,329		162,497
Research and development expenses	Research and development expenses	493,497		555,948		1,362,953		1,274,529		Research and development expenses		455,973		448,528
Sales, general and administrative expenses	Sales, general and administrative expenses	184,551		159,674		558,613		463,221		Sales, general and administrative expenses		192,077		182,258
Change in fair value of contingent consideration	Change in fair value of contingent consideration	1,800		2,959		12,600		2,959		Change in fair value of contingent consideration		(3,900)		1,600
Total costs and expenses	Total costs and expenses	866,030		850,495		2,467,365		2,103,455		Total costs and expenses		836,479		794,883
Income from operations	Income from operations	672,241		99,333		2,110,498		646,101		Income from operations		887,826		720,224
Interest income	Interest income	3,100		17,628		19,919		51,319		Interest income		1,465		12,576
Interest expense	Interest expense	(13,856)		(14,548)		(41,863)		(44,253)		Interest expense		(15,678)		(14,136)
Other income (expense), net		84,386		(31,747)		139,621		64,802
Other expense, net										Other expense, net		(52,653)		(61,130)
Income before provision for income taxes	Income before provision for income taxes	745,871		70,666		2,228,175		717,969		Income before provision for income taxes		820,960		657,534
Provision for income taxes	Provision for income taxes	78,437		13,148		120,718		124,393		Provision for income taxes		167,822		54,781
Net income	Net income	$	667,434	$	57,518	$	2,107,457	$	593,576	Net income		$	653,138	$	602,753

Net income per common share:	Net income per common share:									Net income per common share:
Basic	Basic	$	2.56	$	0.22	$	8.10	$	2.32	Basic		$	2.52	$	2.32
Diluted	Diluted	$	2.53	$	0.22	$	7.98	$	2.28	Diluted		$	2.49	$	2.29
Shares used in per share calculations:	Shares used in per share calculations:									Shares used in per share calculations:
Basic	Basic	260,392		256,946		260,313		256,289		Basic		259,369		259,815
Diluted	Diluted	264,079		260,473		264,031		260,182		Diluted		261,916		263,515

The accompanying notes are an integral part of these condensed consolidated financial statements.

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VERTEX PHARMACEUTICALS INCORPORATED

Condensed Consolidated Statements of Comprehensive Income

(unaudited)

(in thousands)

Three Months Ended September 30, Nine Months Ended September 30,
2020 2019 2020 2019
Net income $ 667,434 $ 57,518 $ 2,107,457 $ 593,576
Other comprehensive (loss) income:
Unrealized holding (losses) gains on marketable securities, net (1,132) 64 818 1,111
Unrealized (losses) gains on foreign currency forward contracts, net of tax of $7.6 million, $2.2 million, $7.3 million and $5.5 million, respectively (26,313) 12,812 (27,211) 6,814
Foreign currency translation adjustment 584 9,172 (12,616) 10,263
Total other comprehensive (loss) income (26,861) 22,048 (39,009) 18,188
Comprehensive income $ 640,573 $ 79,566 $ 2,068,448 $ 611,764


	Three Months Ended March 31,
		2021		2020
Net income		$	653,138	$	602,753
Other comprehensive income:
Unrealized holding losses on marketable securities, net		(218)		(764)
Unrealized gains on foreign currency forward contracts, net of tax of $(9.3) million and $(5.0) million, respectively		33,966		18,782
Foreign currency translation adjustment		1,430		(2,662)
Total other comprehensive income		35,178		15,356
Comprehensive income		$	688,316	$	618,109

The accompanying notes are an integral part of these condensed consolidated financial statements.

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VERTEX PHARMACEUTICALS INCORPORATED

Condensed Consolidated Balance Sheets

(unaudited)

(in thousands, except per share amounts)


		September 30,		December 31,			March 31,		December 31,
		2020		2019			2021		2020
Assets	Assets					Assets
Current assets:	Current assets:					Current assets:
Cash and cash equivalents	Cash and cash equivalents	$	5,358,087	$	3,109,322	Cash and cash equivalents	$	6,304,330	$	5,988,187
Marketable securities	Marketable securities	792,971		698,972		Marketable securities	619,638		670,710
Accounts receivable, net	Accounts receivable, net	791,917		633,518		Accounts receivable, net	977,551		885,352
Inventories	Inventories	245,460		167,502		Inventories	298,863		280,777
Prepaid expenses and other current assets	Prepaid expenses and other current assets	270,021		213,515		Prepaid expenses and other current assets	338,925		308,353
Total current assets	Total current assets	7,458,456		4,822,829		Total current assets	8,539,307		8,133,379
Property and equipment, net	Property and equipment, net	920,913		745,080		Property and equipment, net	986,123		958,534
Goodwill	Goodwill	1,002,158		1,002,158		Goodwill	1,002,158		1,002,158
Intangible assets	Intangible assets	400,000		400,000		Intangible assets	400,000		400,000
Deferred tax assets	Deferred tax assets	1,147,816		1,190,815		Deferred tax assets	815,890		882,779
Operating lease assets						Operating lease assets	322,319		325,564
Other assets	Other assets	372,290		157,583		Other assets	49,262		49,394
Total assets	Total assets	$	11,301,633	$	8,318,465	Total assets	$	12,115,059	$	11,751,808
Liabilities and Shareholders’ Equity	Liabilities and Shareholders’ Equity					Liabilities and Shareholders’ Equity
Current liabilities:	Current liabilities:					Current liabilities:
Accounts payable	Accounts payable	$	107,786	$	87,610	Accounts payable	$	127,839	$	155,139
Accrued expenses	Accrued expenses	1,703,699		1,116,912		Accrued expenses	1,532,037		1,404,971
Other current liabilities	Other current liabilities	192,541		130,305		Other current liabilities	284,174		317,423
Total current liabilities	Total current liabilities	2,004,026		1,334,827		Total current liabilities	1,944,050		1,877,533
Long-term finance lease liabilities	Long-term finance lease liabilities	546,514		538,576		Long-term finance lease liabilities	530,330		539,042
Long-term operating lease liabilities						Long-term operating lease liabilities	368,467		350,463
Long-term contingent consideration	Long-term contingent consideration	189,100		176,500		Long-term contingent consideration	185,700		189,600
Other long-term liabilities	Other long-term liabilities	428,520		183,318		Other long-term liabilities	106,258		108,355
Total liabilities	Total liabilities	3,168,160		2,233,221		Total liabilities	3,134,805		3,064,993
Commitments and contingencies	Commitments and contingencies	0		0		Commitments and contingencies	0		0
Shareholders’ equity:	Shareholders’ equity:					Shareholders’ equity:
Preferred stock, $0.01 par value; 1,000 shares authorized; NaN issued and outstanding	Preferred stock, $0.01 par value; 1,000 shares authorized; NaN issued and outstanding	0		0		Preferred stock, $0.01 par value; 1,000 shares authorized; NaN issued and outstanding	0		0
Common stock, $0.01 par value; 500,000 shares authorized, 260,174 and 258,993 shares issued and outstanding, respectively		2,601		2,589
Common stock, $0.01 par value; 500,000 shares authorized, 258,829 and 259,890 shares issued and outstanding, respectively						Common stock, $0.01 par value; 500,000 shares authorized, 258,829 and 259,890 shares issued and outstanding, respectively	2,588		2,599
Additional paid-in capital	Additional paid-in capital	7,917,375		7,937,606		Additional paid-in capital	7,499,161		7,894,027
Accumulated other comprehensive loss	Accumulated other comprehensive loss	(40,982)		(1,973)		Accumulated other comprehensive loss	(33,302)		(68,480)
Retained earnings (accumulated deficit)		254,479		(1,852,978)
Retained earnings						Retained earnings	1,511,807		858,669
Total shareholders’ equity	Total shareholders’ equity	8,133,473		6,085,244		Total shareholders’ equity	8,980,254		8,686,815
Total liabilities and shareholders’ equity	Total liabilities and shareholders’ equity	$	11,301,633	$	8,318,465	Total liabilities and shareholders’ equity	$	12,115,059	$	11,751,808

The accompanying notes are an integral part of these condensed consolidated financial statements.

Table of Contents

VERTEX PHARMACEUTICALS INCORPORATED

Condensed Consolidated Statements of Shareholders’ Equity

(unaudited)

(in thousands)


		Three Months Ended
		Common Stock			Additional Paid-in Capital				Accumulated Other Comprehensive Income (Loss)		Retained Earnings (Accumulated Deficit)				Total Shareholders’ Equity
		Shares	Amount
Balance at June 30, 2019		256,671	$	2,565			$	7,564,331					$	(3,201)					$	(2,493,730)		$	5,069,965

																		Three Months Ended
																		Common Stock						Additional Paid-in Capital				Accumulated Other Comprehensive Income (Loss)		Retained Earnings (Accumulated Deficit)		Total Shareholders’ Equity
																		Shares			Amount
Balance at December 31, 2019																	Balance at December 31, 2019	258,993			$	2,589				$	7,937,606			$	(1,973)	$	(1,852,978)	$	6,085,244
Other comprehensive income, net of tax	Other comprehensive income, net of tax	—	—		—				22,048		—				22,048		Other comprehensive income, net of tax	—			—			—				15,356		—		15,356
Net income	Net income	—	—		—				—		57,518				57,518		Net income	—			—			—				—		602,753		602,753
Repurchase of common stock	Repurchase of common stock	(71)	—		(12,001)				—		—				(12,001)		Repurchase of common stock	(1,404)			(14)			(300,012)				—		—		(300,026)
Common stock withheld for employee tax obligations	Common stock withheld for employee tax obligations	—	—		(104)				—		—				(104)		Common stock withheld for employee tax obligations	(575)			(6)			(136,161)				—		—		(136,167)
Issuance of common stock under benefit plans	Issuance of common stock under benefit plans	665	6		30,006				—		—				30,012		Issuance of common stock under benefit plans	2,065			22			77,572				—		—		77,594
Stock-based compensation expense	Stock-based compensation expense	—	—		85,956				—		—				85,956		Stock-based compensation expense	—			—			116,900				—		—		116,900
Balance at September 30, 2019		257,265	$	2,571	$	7,668,188			$	18,847	$	(2,436,212)			$	5,253,394
Balance at March 31, 2020																	Balance at March 31, 2020	259,079			$	2,591		$	7,695,905			$	13,383	$	(1,250,225)	$	6,461,654

Balance at June 30, 2020		260,124	$	2,601	$	7,943,717			$	(14,121)	$	(412,955)			$	7,519,242
Other comprehensive loss, net of tax		—	—		—				(26,861)		—				(26,861)
Net income		—	—		—				—		667,434				667,434
Repurchase of common stock		(403)	(4)		(108,003)				—		—				(108,007)
Common stock withheld for employee tax obligations		(141)	(1)		(40,527)				—		—				(40,528)
Issuance of common stock under benefit plans		594	5		21,699				—		—				21,704
Stock-based compensation expense		—	—		100,489				—		—				100,489
Balance at September 30, 2020		260,174	$	2,601	$	7,917,375			$	(40,982)	$	254,479			$	8,133,473

		Nine Months Ended
		Common Stock			Additional Paid-in Capital				Accumulated Other Comprehensive Income (Loss)		Retained Earnings (Accumulated Deficit)				Total Shareholders’ Equity
		Shares	Amount
Balance at December 31, 2018		255,172	$	2,546			$	7,421,476					$	659					$	(2,989,478)		$	4,435,203
Cumulative effect adjustment for adoption of new accounting guidance		—	—		—				—		(40,310)				(40,310)
Balance at December 31, 2020																	Balance at December 31, 2020	259,890			$	2,599		$	7,894,027			$	(68,480)	$	858,669	$	8,686,815
Other comprehensive income, net of tax	Other comprehensive income, net of tax	—	—		—				18,188		—				18,188		Other comprehensive income, net of tax	—			—			—				35,178		—		35,178
Net income	Net income	—	—		—				—		593,576				593,576		Net income	—			—			—				—		653,138		653,138
Repurchase of common stock	Repurchase of common stock	(904)	(9)		(162,009)				—		—				(162,018)		Repurchase of common stock	(1,989)			(20)			(424,932)				—		—		(424,952)
Common stock withheld for employee tax obligations	Common stock withheld for employee tax obligations	(27)	—		(5,936)				—		—				(5,936)		Common stock withheld for employee tax obligations	(472)			(5)			(102,135)				—		—		(102,140)
Issuance of common stock under benefit plans	Issuance of common stock under benefit plans	3,024	34		144,523				—		—				144,557		Issuance of common stock under benefit plans	1,400			14			15,164				—		—		15,178
Stock-based compensation expense	Stock-based compensation expense	—	—		270,134				—		—				270,134		Stock-based compensation expense	—			—			117,037				—		—		117,037
Balance at September 30, 2019		257,265	$	2,571	$	7,668,188			$	18,847	$	(2,436,212)			$	5,253,394

Balance at December 31, 2019		258,993	$	2,589	$	7,937,606			$	(1,973)	$	(1,852,978)			$	6,085,244
Other comprehensive loss, net of tax		—	—		—				(39,009)		—				(39,009)
Net income		—	—		—				—		2,107,457				2,107,457
Repurchase of common stock		(1,807)	(18)		(408,015)				—		—				(408,033)
Common stock withheld for employee tax obligations		(727)	(7)		(179,768)										(179,775)
Issuance of common stock under benefit plans		3,715	37		232,042				—		—				232,079
Stock-based compensation expense		—	—		335,510				—		—				335,510
Balance at September 30, 2020		260,174	$	2,601	$	7,917,375			$	(40,982)	$	254,479			$	8,133,473
Balance at March 31, 2021																	Balance at March 31, 2021	258,829			$	2,588		$	7,499,161			$	(33,302)	$	1,511,807	$	8,980,254

The accompanying notes are an integral part of these condensed consolidated financial statements.

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VERTEX PHARMACEUTICALS INCORPORATED

Condensed Consolidated Statements of Cash Flows

(unaudited)

(in thousands)


		Nine Months Ended September 30,					Three Months Ended March 31,
		2020		2019			2021		2020
Cash flows from operating activities:	Cash flows from operating activities:					Cash flows from operating activities:
Net income	Net income	$	2,107,457	$	593,576	Net income	$	653,138	$	602,753
Adjustments to reconcile net income to net cash provided by operating activities:	Adjustments to reconcile net income to net cash provided by operating activities:					Adjustments to reconcile net income to net cash provided by operating activities:
Stock-based compensation expense	Stock-based compensation expense	332,434		268,898		Stock-based compensation expense	115,174		115,706
Depreciation expense	Depreciation expense	80,160		80,685		Depreciation expense	28,834		26,821
Increase in fair value of contingent consideration		12,600		2,959
(Decrease) increase in fair value of contingent consideration						(Decrease) increase in fair value of contingent consideration	(3,900)		1,600
Deferred income taxes	Deferred income taxes	65,110		94,175		Deferred income taxes	57,043		36,705
Gains on equity securities		(140,866)		(68,862)
Losses on equity securities						Losses on equity securities	52,295		44,870
Other non-cash items, net	Other non-cash items, net	52,371		(4,024)		Other non-cash items, net	2,332		9,668
Changes in operating assets and liabilities:	Changes in operating assets and liabilities:					Changes in operating assets and liabilities:
Accounts receivable, net	Accounts receivable, net	(151,191)		(41,444)		Accounts receivable, net	(98,373)		(223,672)
Inventories	Inventories	(94,907)		(45,280)		Inventories	(22,785)		(27,450)
Prepaid expenses and other assets	Prepaid expenses and other assets	(264,909)		(23,709)		Prepaid expenses and other assets	(13,319)		2,790
Accounts payable	Accounts payable	16,153		(12,210)		Accounts payable	(10,644)		14,285
Accrued expenses	Accrued expenses	451,084		255,699		Accrued expenses	152,983		153,814
Other liabilities	Other liabilities	296,477		22,859		Other liabilities	8,277		57,808
Net cash provided by operating activities	Net cash provided by operating activities	2,761,973		1,123,322		Net cash provided by operating activities	921,055		815,698
Cash flows from investing activities:	Cash flows from investing activities:					Cash flows from investing activities:
Purchases of available-for-sale debt securities	Purchases of available-for-sale debt securities	(246,937)		(381,739)		Purchases of available-for-sale debt securities	(121,455)		(75,265)
Maturities of available-for-sale debt securities	Maturities of available-for-sale debt securities	184,419		375,145		Maturities of available-for-sale debt securities	118,072		60,145
Sale of equity securities	Sale of equity securities	149,595		0		Sale of equity securities	0		72,036
Payment to acquire business, net of cash acquired		0		(245,824)
Expenditures for property and equipment		(212,109)		(58,690)
Purchases of property and equipment						Purchases of property and equipment	(70,926)		(19,450)
Investment in equity securities	Investment in equity securities	(19,327)		(27,219)		Investment in equity securities	0		(5,800)
Net cash used in investing activities		(144,359)		(338,327)
Net cash (used in) provided by investing activities						Net cash (used in) provided by investing activities	(74,309)		31,666
Cash flows from financing activities:	Cash flows from financing activities:					Cash flows from financing activities:
Issuances of common stock under benefit plans	Issuances of common stock under benefit plans	234,854		144,630		Issuances of common stock under benefit plans	15,559		79,597
Repurchases of common stock	Repurchases of common stock	(408,033)		(150,017)		Repurchases of common stock	(424,952)		(300,026)
Payments in connection with common stock withheld for employee tax obligations	Payments in connection with common stock withheld for employee tax obligations	(179,775)		(5,936)		Payments in connection with common stock withheld for employee tax obligations	(102,140)		(136,167)
Payments on finance leases	Payments on finance leases	(31,378)		(28,879)		Payments on finance leases	(12,233)		(10,287)
Proceeds related to finance leases		8,642		1,002
Advance from collaborator		5,000		10,000
Repayments of advanced funding		(2,741)		(4,316)
Proceeds from finance leases						Proceeds from finance leases	3,632		5,833
Other financing activities	Other financing activities	(6,658)		(1,132)		Other financing activities	1,480		1,620
Net cash used in financing activities	Net cash used in financing activities	(380,089)		(34,648)		Net cash used in financing activities	(518,654)		(359,430)
Effect of changes in exchange rates on cash	Effect of changes in exchange rates on cash	2,779		(4,009)		Effect of changes in exchange rates on cash	(4,030)		(6,651)
Net increase in cash and cash equivalents		2,240,304		746,338
Net increase in cash, cash equivalents and restricted cash						Net increase in cash, cash equivalents and restricted cash	324,062		481,283
Cash, cash equivalents and restricted cash—beginning of period	Cash, cash equivalents and restricted cash—beginning of period	3,120,681		2,658,253		Cash, cash equivalents and restricted cash—beginning of period	5,988,845		3,120,681
Cash, cash equivalents and restricted cash—end of period	Cash, cash equivalents and restricted cash—end of period	$	5,360,985	$	3,404,591	Cash, cash equivalents and restricted cash—end of period	$	6,312,907	$	3,601,964

Supplemental disclosure of cash flow information:	Supplemental disclosure of cash flow information:					Supplemental disclosure of cash flow information:
Cash paid for interest	Cash paid for interest	$	40,769	$	41,704	Cash paid for interest	$	14,534	$	13,771
Cash paid for income taxes	Cash paid for income taxes	$	81,684	$	22,838	Cash paid for income taxes	$	10,691	$	5,845
Issuances of common stock from employee benefit plans receivable		$	45	$	13
Accrued share repurchase liability		$	0	$	12,001

The accompanying notes are an integral part of these condensed consolidated financial statements.

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements

(unaudited)

A.Basis of Presentation and Accounting Policies

Basis of Presentation

The accompanying condensed consolidated financial statements are unaudited and have been prepared by Vertex Pharmaceuticals Incorporated (“Vertex” or the “Company”) in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”).

The condensed consolidated financial statements reflect the operations of the Company and its wholly-owned subsidiaries. All material intercompany balances and transactions have been eliminated. The Company operates in 1 segment, pharmaceuticals. The Company has reclassified certain items from the prior year’s condensed consolidated financial statements to conform to the current year’s presentation.

Certain information and footnote disclosures normally included in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, ~~2019~~2020 (the ~~“2019~~“2020 Annual Report on Form 10-K”) have been condensed or omitted. These interim financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for a fair presentation of the financial position and results of operations for the interim periods ended ~~September 30, 2020~~March 31, 2021 and ~~2019.~~2020.

The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the full fiscal year. These interim financial statements should be read in conjunction with the audited financial statements for the year ended December 31, ~~2019,~~2020, which are contained in the Company’s ~~2019~~2020 Annual Report on Form 10-K.

Use of Estimates

The preparation of condensed consolidated financial statements in accordance with U.S. GAAP requires management to make certain estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. Significant estimates in these condensed consolidated financial statements have been made in connection with (i) determining the transaction price of revenues and (ii) accounting for intangible assets and contingent consideration. The Company bases its estimates on historical experience and various other assumptions, including in certain circumstances future projections that management believes to be reasonable under the circumstances. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known.

Recently Adopted ~~Accounting Standards~~

~~Leases~~

~~On January 1, 2019, the Company adopted Accounting Standards Codification (“ASC”) 842,~~ ~~Leases~~ (“~~ASC 842”) using the modified-retrospective method, which amended a number of aspects of lease accounting~~ and required the Company to recognize right-of-use assets and liabilities on the balance sheet. As of January 1, 2019, the Company recorded a cumulative effect adjustment to increase its “Accumulated deficit” by $40.3 million, which related to its leases that were accounted for as build-to-suit leases under the previous accounting guidance.

~~Internal-Use Software~~

~~In 2018, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) 2018-15,~~ ~~Intangibles—Goodwill and Other—Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract~~ (“ASU 2018-15”), which clarifies the accounting for implementation costs in cloud computing arrangements. ASU 2018-15 became effective on January 1, 2020. The adoption of ASU 2018-15 resulted in an insignificant amount of additional assets recorded on the Company’s condensed consolidated balance sheet.

~~Table of Contents~~

~~VERTEX PHARMACEUTICALS INCORPORATED~~

~~Notes to Condensed Consolidated Financial Statements~~

~~(unaudited)~~

~~Fair Value Measurement~~

~~In 2018, the FASB issued ASU 2018-13,~~ ~~Fair Value Measurement (Topic 820): Disclosure Framework-Changes to the Disclosure Requirements for Fair Value Measurement~~ (“ASU 2018-13”), which modifies the disclosure requirements for fair value measurements. ASU 2018-13 became effective on January 1, 2020. The adoption of ASU 2018-13 resulted in additional disclosures related to the Company’s Level 3 inputs. Please refer to Note E, “Fair Value Measurements,” for further information.

~~Credit Losses~~

~~In 2016, the FASB issued ASU 2016-13,~~ ~~Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments~~ (“ASU 2016-13”), which requires entities to record expected credit losses for certain financial instruments, including trade receivables, as an allowance that reflects the entity's current estimate of credit losses expected to be incurred. For available-for-sale debt securities in unrealized loss positions, ASU 2016-13 requires allowances to be recorded instead of reducing the amortized cost of the investment. ASU 2016-13 became effective on January 1, 2020. The adoption of ASU 2016-13 did not have a significant impact on the Company’s condensed consolidated financial statements.

~~Recently~~ Issued Accounting Standards

Income Taxes

In 2019, the FASB issued ASU 2019-12, Income Taxes (Topic 740) (“ASU 2019-12”), which simplifies the accounting for income taxes. ASU 2019-12 isbecame effective on January 1, 2021. The ~~Company is evaluating the impact the~~ adoption of ASU 2019-12 ~~may~~did not have a significant impact on ~~its~~the Company’s condensed consolidated financial statements.

For a discussion of other recent accounting pronouncements please refer to Note A, “Nature of Business and Accounting Policies,” in the Company’s ~~2019~~2020 Annual Report on Form 10-K.

Summary of Significant Accounting Policies

The Company’s significant accounting policies are described in Note A, “Nature of Business and Accounting Policies,” in its ~~2019~~2020 Annual Report on Form 10-K.

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements (unaudited)

B.Revenue Recognition

Disaggregation of Revenue

Revenues by Product

Product revenues, net consisted of the following:


		Three Months Ended September 30,				Nine Months Ended September 30,					Three Months Ended March 31,
		2020		2019		2020		2019				2021		2020
		(in thousands)										(in thousands)
TRIKAFTA/KAFTRIO	TRIKAFTA/KAFTRIO	$	960,308	$	0	$	2,773,256	$	0	TRIKAFTA/KAFTRIO		$	1,193,217	$	895,233
SYMDEKO/SYMKEVI	SYMDEKO/SYMKEVI	156,178		403,714		501,066		1,085,821		SYMDEKO/SYMKEVI		125,049		173,159
ORKAMBI	ORKAMBI	225,919		296,711		692,038		906,159		ORKAMBI		218,697		234,138
KALYDECO	KALYDECO	193,866		249,403		609,503		755,481		KALYDECO		186,342		212,577
Total product revenues, net*		$	1,536,271	$	949,828	$	4,575,863	$	2,747,461
Total product revenues, net										Total product revenues, net		$	1,723,305	$	1,515,107

* ~~The preceding table does not include collaborative and royalty revenues.~~

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~~VERTEX PHARMACEUTICALS INCORPORATED~~

~~Notes to Condensed Consolidated Financial Statements~~

~~(unaudited)~~

Product Revenues by Geographic Location

~~Net~~Total net product revenues ~~are attributed to countries~~by geographic region, based on the location of the customer. Collaborative and royalty revenues outside of the United States are attributed to countries based on the location of the Company’s subsidiary associated with the collaborative arrangement related to such revenues. Total revenues from external customers and collaborators by geographic regioncustomer, consisted of the following:


		Three Months Ended September 30,				Nine Months Ended September 30,					Three Months Ended March 31,
		2020		2019		2020		2019				2021		2020
		(in thousands)										(in thousands)
United States	United States	$	1,224,565	$	710,323	$	3,622,467	$	2,052,044	United States		$	1,253,433	$	1,187,588
Outside of the United States	Outside of the United States									Outside of the United States
Europe	Europe	251,366		184,845		766,438		532,809		Europe		404,969		257,391
Other	Other	62,340		54,660		188,958		164,703		Other		64,903		70,128
Total revenues outside of the United States		313,706		239,505		955,396		697,512
Total revenues		$	1,538,271	$	949,828	$	4,577,863	$	2,749,556
Total product revenues outside of the United States										Total product revenues outside of the United States		469,872		327,519
Total product revenues, net										Total product revenues, net		$	1,723,305	$	1,515,107

Contract Liabilities

The Company had contract liabilities of ~~$94.8~~$181.2 million and ~~$62.3~~$191.5 million as of ~~September 30, 2020~~March 31, 2021 and December 31, ~~2019,~~2020, respectively, related to annual contracts with government-owned and supported customers in international markets that limit the amount of annual reimbursement the Company can receive. Upon exceeding the annual reimbursement amount, products are provided free of charge, which is a material right. These contracts include upfront payments and fees. The Company defers a portion of the consideration received for shipments made up to the annual reimbursement limit as a portion of “Other current liabilities.” The deferred amount is recognized as revenue when the free products are shipped. The Company’s product revenue contracts include performance obligations that are one year or less.

The Company’s contract liabilities at the end of each fiscal year relate to contracts with annual reimbursement limits in international markets in which the annual period associated with the contract is not the same as the Company’s fiscal year. In these markets, the Company recognizes revenues related to performance obligations satisfied in previous years; however, these revenues do not relate to any performance obligations that were satisfied more than 12 months prior to the beginning of the current year.

C.Collaborative Arrangements

The Company has entered into numerous agreements pursuant to which it collaborates with third parties on research, development and commercialization programs, including in-license and out-license agreements.

The Company’s in-license and out-license agreements that had a significant impact on its financial statements for the three ~~and nine~~ months ended ~~September 30,~~March 31, 2021 and 2020, ~~and 2019,~~ or were new or otherwise revised during the three ~~and nine~~ months ended ~~September 30, 2020,~~March 31,

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements (unaudited)

2021, are described below. Additional in-license and out-license agreements were described in Note B, “Collaborative Arrangements,” of the Company’s ~~2019~~2020 Annual Report on Form 10-K.

In-license Agreements

The Company has entered into a number of license agreements in order to advance and obtain access to technologies and services related to its research and early-development activities. The Company is generally required to make an upfront payment upon execution of the license agreement; development, regulatory and commercialization milestones payments upon the achievement of certain product research, development and commercialization objectives; and royalty payments on future sales, if any, of commercial products resulting from the collaboration.

~~Table of Contents~~

~~VERTEX PHARMACEUTICALS INCORPORATED~~

~~Notes to Condensed Consolidated Financial Statements~~

~~(unaudited)~~

Pursuant to the terms of its in-license agreements, the Company’s collaborators typically lead the discovery efforts and the Company leads all preclinical, development and commercialization activities associated with the advancement of any drug candidates and funds all expenses.

The Company typically can terminate its in-license agreements by providing advance notice to its collaborators; the required length of notice is dependent on whether any product developed under the license agreement has received marketing approval. The Company’s license agreements may be terminated by either party for a material breach by the other, subject to notice and cure provisions. Unless earlier terminated, these license agreements generally remain in effect until the date on which the royalty term and all payment obligations with respect to all products in all countries have expired.

CRISPR Therapeutics AG - CRISPR-Cas9 Gene-editing Therapies

In 2015, the Company entered into a strategic collaboration, option and license agreement (the “CRISPR Agreement”) with CRISPR Therapeutics AG and its affiliates (“CRISPR”) to collaborate on the discovery and development of potential new treatments aimed at the underlying genetic causes of human diseases using CRISPR-Cas9 gene-editing technology. The Company had the exclusive right to license certain targets. In ~~the fourth quarter of~~ 2019, the Company elected to exclusively license 3 targets, including cystic fibrosis, pursuant to the CRISPR Agreement. For each of the 3 targets that the Company elected to license, CRISPR has the potential to receive up to an additional $410.0 million in development, regulatory and commercial milestones as well as royalties on net product sales.

In 2017, the Company entered into a ~~co-development~~joint development and ~~co-commercialization~~commercialization agreement with CRISPR pursuant to the terms of the CRISPR Agreement (the “Original CTX001 JDCA”), under which the Company and CRISPR are co-developing and ~~will~~preparing to co-commercialize CTX001 ~~(the “CTX001 Co-Co Agreement”)~~ for the treatment of hemoglobinopathies, including treatments for sickle cell disease and beta thalassemia. ~~As part of the collaboration, the Company and CRISPR share equally all development costs and potential worldwide revenues related to potential hemoglobinopathy treatments.~~ The Company concluded that the Original CTX001 ~~Co-Co Agreement~~JDCA is a cost-sharing arrangement, which results in the net impact of the arrangement being recorded in “Research and development expenses” in its condensed consolidated statements of operations. During the three ~~and nine~~ months ended ~~September 30,~~March 31, 2021 and 2020, the net expense related to the Original CTX001 ~~Co-Co Agreement~~JDCA was ~~$14.3~~$20.0 million and ~~$33.4 million, respectively. During the three and nine months ended September 30, 2019, the net expense related to the CTX001 Co-Co Agreement was $7.7 million and $22.3~~$9.3 million, respectively.

In July 2019, the Company entered into a separate strategic collaboration and license agreement (the “CRISPR DMD/DM1 Agreement”) with CRISPR. Pursuant to this agreement, the Company received an exclusive worldwide license to CRISPR’s existing and future intellectual property for Duchenne muscular dystrophy (“DMD”) and myotonic dystrophy type 1 (“DM1”) and the Company made an upfront payment of $175.0 million to CRISPR. The Company concluded that it did not have any alternative future use for the acquired in-process research and development and recorded the upfront payment to “Research and development expenses” in the third quarter of 2019. In the first quarter of 2020, the Company recorded $25.0 million to “Research and development expenses” related to a pre-clinical milestone earned by CRISPR under the CRISPR DMD/DM1 Agreement. CRISPR has the potential to receive up to an additional $800.0 million in research, development, regulatory and commercial milestones for the DMD and DM1 programs as well as royalties on net product sales. CRISPR has the option to co-develop and co-commercialize all DM1 products globally and forego the milestones and royalties associated with the DM1 program. The Company funds all expenses associated with the collaboration except for research costs for specified guide RNA research conducted by CRISPR, whichApril 2021, the Company and CRISPR ~~share equally.~~

~~Moderna, Inc.~~

~~In 2016,~~amended and restated the ~~Company entered into a strategic collaboration and licensing agreement with Moderna, Inc. (“Moderna”~~Original CTX001 JDCA (the “A&R JDCA”), pursuant to which the parties ~~are seeking~~agreed to, ~~identify and develop messenger Ribonucleic Acid (“mRNA”) therapeutics~~among other things, (a) adjust the governance structure for the ~~treatment~~collaboration and adjust the responsibilities of ~~cystic fibrosis.~~

~~In September 2020,~~each party thereunder; (b) adjust the allocation of net profits and net losses between the parties; and (c) exclusively license (subject to CRISPR’s reserved rights to conduct certain activities) certain intellectual property rights to the Company entered into a new strategic collaboration and licensing agreement with Moderna (the “2020 Moderna Agreement”) aimed at the discovery and development of lipid nanoparticles and mRNAs that can deliver gene-editing therapies to lung cells for the treatment of cystic fibrosis. Pursuantrelating to the ~~2020 Moderna Agreement, Moderna received an upfront payment of $75.0 million~~products that may be researched, developed, manufactured and ~~is eligible to receive up to $380.0 million in development, regulatory and commercial milestones as well as royalties on net product sales.~~commercialized under such agreement. The ~~Company determined that substantially all~~closing of the ~~fair~~transaction contemplated under the A&R JDCA is subject to certain conditions, including the expiration of the waiting period under the Hart-Scott-Rodino Antitrust Improvements Act and any other required antitrust clearance.

After the effective date of the closing of the transaction (the “Effective Date”), the Company will lead global development, manufacturing and commercialization of CTX001, with support from CRISPR. Subject to the terms and conditions of the A&R JDCA, the Company will have the right to conduct all research, development, manufacturing and commercialization activities relating to the product candidates and products under the A&R JDCA (including CTX001) throughout the world subject to CRISPR’s reserved right to conduct certain activities.

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements

(unaudited)

~~value~~In connection with the closing of the ~~2020 Moderna Agreement was attributable~~transaction contemplated by the A&R JDCA, the Company will pay a $900.0 million upfront payment to ~~in-process research~~CRISPR and ~~development and no substantive processes were acquired that would constitute a business.~~an additional one-time $200.0 million milestone payment upon receipt of the first marketing approval of CTX001 from the U.S. Food or Drug Administration or the European Commission. The Company ~~concluded that it did not~~and CRISPR will continue to share equally all net profits and net losses incurred under the A&R JDCA through June 30, 2021, subject to adjustment based on the timing of antitrust clearance. Beginning July 1, 2021 (or the first day of the calendar quarter in which antitrust clearance occurs), with respect to CTX001, the net profits and net losses incurred pursuant to the A&R JDCA will be allocated 60% to the Company and 40% to CRISPR, while all other product candidate and products will continue to have ~~any alternative future use for~~net profits and net losses shared equally. The Company expects to record the ~~acquired in-process research and development and recorded the~~$900.0 million upfront payment to “Research and development expenses” inupon closing of the ~~third quarter of 2020.~~transaction contemplated by the A&R JDCA.

Out-license Agreements

The Company has entered into licensing agreements pursuant to which it has out-licensed rights to certain drug candidates to third-party collaborators. Pursuant to these out-license agreements, the Company’s collaborators become responsible for all costs related to the continued development of such drug candidates and obtain development and commercialization rights to these drug candidates. Depending on the terms of the agreements, the Company’s collaborators may be required to make upfront payments, milestone payments upon the achievement of certain product research and development objectives and may also be required to pay royalties on future sales, if any, of commercial products resulting from the collaboration. The termination provisions associated with these collaborations are generally the same as those described above related to the Company’s in-license agreements. None of the Company’s out-license agreements had a significant impact on the Company’s condensed consolidated statement of operations during the three ~~and nine~~ months ended ~~September 30, 2020~~March 31, 2021 and ~~2019.~~2020.

~~Janssen Pharmaceuticals, Inc.~~

In the third quarter of 2020, Janssen Pharmaceuticals, Inc. (“Janssen”) exercised its right to terminate its exclusive worldwide license from the Company to develop and commercialize certain drug candidates for the treatment of influenza, based on Phase 3 clinical trial results for pimodivir. Janssen had been developing pimodivir since 2014.

Cystic Fibrosis Foundation

The Company has a research, development and commercialization agreement that was originally entered into in 2004 with the Cystic Fibrosis Foundation, ~~(“CFF”),~~ as successor in interest to the Cystic Fibrosis Foundation Therapeutics, Inc. This agreement was most recently amended in 2016. Pursuant to the agreement, as amended, the Company agreed to pay royalties ranging from low-single digits to mid-single digits on potential sales of certain compounds first synthesized and/or tested between March 1, 2014 and August 31, 2016, including elexacaftor, and tiered royalties ranging from single digits to sub-teens on covered compounds first synthesized and/or tested during a research term on or before February 28, 2014, including KALYDECO (ivacaftor), ORKAMBI (lumacaftor in combination with ivacaftor) and SYMDEKO/SYMKEVI (tezacaftor in combination with ivacaftor). For combination products, such as ORKAMBI, SYMDEKO/SYMKEVI and TRIKAFTA/KAFTRIO (elexacaftor/tezacaftor/ivacaftor and ivacaftor), sales are allocated equally to each of the active pharmaceutical ingredients in the combination product.

D.Earnings Per Share

Basic net income per common share is based upon the weighted-average number of common shares ~~outstanding.~~outstanding during the period. Diluted net income per common share utilizing the ~~treasury~~treasury-stock method is based upon the weighted-average number of common shares outstanding during the period plus additional weighted-average common equivalent shares outstanding during the period when the effect is dilutive.

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements

(unaudited)

The following table sets forth the computation of basic and diluted net income per common share for the periods ended:


		Three Months Ended September 30,				Nine Months Ended September 30,					Three Months Ended March 31,
		2020		2019		2020		2019				2021		2020
		(in thousands, except per share amounts)										(in thousands, except per share amounts)
Net income	Net income	$	667,434	$	57,518	$	2,107,457	$	593,576	Net income		$	653,138	$	602,753

Basic weighted-average common shares outstanding	Basic weighted-average common shares outstanding	260,392		256,946		260,313		256,289		Basic weighted-average common shares outstanding		259,369		259,815
Effect of potentially dilutive securities:	Effect of potentially dilutive securities:									Effect of potentially dilutive securities:
Stock options	Stock options	1,887		2,080		1,936		2,297		Stock options		1,263		1,868
Restricted stock and restricted stock units (including PSUs)		1,788		1,434		1,765		1,582
Restricted stock units (including PSUs)										Restricted stock units (including PSUs)		1,276		1,801
Employee stock purchase program	Employee stock purchase program	12		13		17		14		Employee stock purchase program		8		31
Diluted weighted-average common shares outstanding	Diluted weighted-average common shares outstanding	264,079		260,473		264,031		260,182		Diluted weighted-average common shares outstanding		261,916		263,515

Basic net income per common share	Basic net income per common share	$	2.56	$	0.22	$	8.10	$	2.32	Basic net income per common share		$	2.52	$	2.32
Diluted net income per common share	Diluted net income per common share	$	2.53	$	0.22	$	7.98	$	2.28	Diluted net income per common share		$	2.49	$	2.29

The Company did not include the securities in the following table in the computation of the net income per common share because the effect would have been anti-dilutive during each period:


		Three Months Ended September 30,		Nine Months Ended September 30,			Three Months Ended March 31,
		2020	2019	2020	2019			2021	2020
		(in thousands)						(in thousands)
Stock options	Stock options	23	3,303	303	3,116	Stock options		356	879
Unvested restricted stock and restricted stock units (including PSUs)		252	13	229	7
Unvested restricted stock units (including PSUs)						Unvested restricted stock units (including PSUs)		712	430

E.Fair Value Measurements

The following fair value hierarchy is used to classify assets and liabilities based on observable inputs and unobservable inputs used in order to determine the fair value of the Company’s financial assets and liabilities:


Level 1:			Quoted prices in active markets for identical assets or liabilities. An active market for an asset or liability is a market in which transactions for the asset or liability occur with sufficient frequency and volume to provide pricing information on an ongoing basis.
Level 2:			Observable inputs other than Level 1 inputs. Examples of Level 2 inputs include quoted prices in active markets for similar assets or liabilities and quoted prices for identical assets or liabilities in markets that are not active.
Level 3:			Unobservable inputs based on the Company’s assessment of the assumptions that market participants would use in pricing the asset or liability.

The Company’s investment strategy is focused on capital preservation. The Company invests in instruments that meet the credit quality standards outlined in the Company’s investment policy. This policy also limits the amount of credit exposure to any one issue or type of instrument. The Company maintains strategic investments separately from the investment policy that governs its other cash, cash equivalents and marketable securities as described in Note F, “Marketable Securities and Equity Investments.” Additionally, the Company utilizes foreign currency forward contracts intended to mitigate the effect of changes in foreign exchange rates on its condensed consolidated statement of operations.

During the three ~~and nine~~ months ended ~~September 30,~~March 31, 2021 and 2020, ~~and 2019,~~ the Company did not record any other-than-temporary impairment charges related to its financial assets.

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Notes to Condensed Consolidated Financial Statements

(unaudited)

The following tables set forth the Company’s financial assets and liabilities subject to fair value measurements by level within the fair value hierarchy (and does not include ~~$2.2~~$2.4 billion and ~~$2.3~~$2.8 billion of cash as of ~~September 30, 2020~~March 31, 2021 and December 31, ~~2019,~~2020, respectively):


		As of September 30, 2020								As of December 31, 2019									As of March 31, 2021									As of December 31, 2020
		Total		Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3			Total		Level 1		Level 2			Level 3		Total		Level 1		Level 2		Level 3
		(in thousands)																	(in thousands)
Financial instruments carried at fair value (asset positions):
Cash equivalents:	Cash equivalents:																	Cash equivalents:
Money market funds	Money market funds	$	3,130,364	$	3,130,364	$	0	$	0	$	791,039	$	791,039	$	0	$	0	Money market funds	$	3,890,303	$	3,890,303	$	0		$	0	$	3,141,053	$	3,141,053	$	0	$	0
Corporate debt securities		0		0		0		0		6,070		0		6,070		0
Commercial paper		5,001		0		5,001		0		29,472		0		29,472		0
Marketable securities:	Marketable securities:																	Marketable securities:
Corporate equity securities	Corporate equity securities	312,682		216,142		96,540		0		282,084		261,797		20,287		0		Corporate equity securities	143,486		143,486		0			0		195,781		15,650		180,131		0
Government-sponsored enterprise securities	Government-sponsored enterprise securities	91,283		91,283		0		0		12,733		12,733		0		0		Government-sponsored enterprise securities	62,362		62,362		0			0		80,063		80,063		0		0
Corporate debt securities	Corporate debt securities	276,610		0		276,610		0		301,799		0		301,799		0		Corporate debt securities	155,716		0		155,716			0		231,598		0		231,598		0
Commercial paper	Commercial paper	112,396		0		112,396		0		102,356		0		102,356		0		Commercial paper	258,074		0		258,074			0		163,268		0		163,268		0
Prepaid expenses and other current assets:	Prepaid expenses and other current assets:																	Prepaid expenses and other current assets:
Foreign currency forward contracts																		Foreign currency forward contracts	7,039		0		7,039			0		0		0		0		0
Other assets:																		Other assets:
Foreign currency forward contracts	Foreign currency forward contracts	673		0		673		0		9,725		0		9,725		0		Foreign currency forward contracts	1,944		0		1,944			0		0		0		0		0
Total financial assets	Total financial assets	$	3,929,009	$	3,437,789	$	491,220	$	0	$	1,535,278	$	1,065,569	$	469,709	$	0	Total financial assets	$	4,518,924	$	4,096,151	$	422,773		$	0	$	3,811,763	$	3,236,766	$	574,997	$	0
																									Financial instruments carried at fair value (liability positions):
Other current liabilities:	Other current liabilities:																	Other current liabilities:
Foreign currency forward contracts	Foreign currency forward contracts	$	(29,554)	$	0	$	(29,554)	$	0	$	(5,533)	$	0	$	(5,533)	$	0	Foreign currency forward contracts	$	(28,743)	$	0	$	(28,743)		$	0	$	(59,184)	$	0	$	(59,184)	$	0
Long-term contingent consideration	Long-term contingent consideration	(189,100)		0		0		(189,100)		(176,500)		0		0		(176,500)		Long-term contingent consideration	(185,700)		0		0			(185,700)		(189,600)		0		0		(189,600)
Other long-term liabilities:	Other long-term liabilities:																	Other long-term liabilities:
Foreign currency forward contracts	Foreign currency forward contracts	(3,254)		0		(3,254)		0		(1,821)		0		(1,821)		0		Foreign currency forward contracts	(433)		0		(433)			0		(4,283)		0		(4,283)		0
Total financial liabilities	Total financial liabilities	$	(221,908)	$	0	$	(32,808)	$	(189,100)	$	(183,854)	$	0	$	(7,354)	$	(176,500)	Total financial liabilities	$	(214,876)	$	0	$	(29,176)		$	(185,700)	$	(253,067)	$	0	$	(63,467)	$	(189,600)

Please refer to Note F, “Marketable Securities and Equity Investments,” for the carrying amount and related unrealized gains (losses) by type of investment.

Fair Value of Corporate Equity Securities

The Company ~~maintains strategic investments in corporate equity securities separately from the investment policy that governs its other cash, cash equivalents and marketable securities. The Company~~ classifies its investments in publicly traded ~~companies~~corporate equity securities as “Marketable securities” on its condensed consolidated balance sheets. Generally, the Company’s investments in the common stock of these publicly traded companies are valued based on Level 1 inputs because they have readily determinable fair values. However, certain of the Company’s investments in publicly traded companies have been or continue to be valued based on Level 2 inputs due to transfer restrictions associated with these investments. Please refer to Note F, “Marketable Securities and Equity Investments,” for further information on these investments.

Fair Value of Contingent Consideration

In 2019, the Company acquired Exonics Therapeutics, Inc. (“Exonics”), a privately-held company focused on creating transformative gene-editing therapies to repair mutations that cause DMD and other severe neuromuscular diseases, including DM1. The Company’s Level 3 contingent consideration liabilities are related to $678.3 million of development and regulatory milestones potentially payable to Exonics’ former equity holders. The Company bases its estimates of the probability of achieving the milestones relevant to the fair value of contingent payments on industry data attributable to rare diseases. The discount rates used in the valuation model for contingent payments, which were between 0.6% and ~~1.9%~~2.4% as of ~~September 30, 2020,~~March 31, 2021, represent a measure of credit risk and market risk associated with settling the liabilities. Significant judgment is used in determining the appropriateness of these assumptions at each reporting period. Due to the uncertainties associated with development and commercialization of drug candidates in the pharmaceutical industry and the effects of

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements

(unaudited)

~~associated with development and commercialization of drug candidates in the pharmaceutical industry and the effects of~~ changes in other assumptions including discount rates, the Company expects its estimates regarding the fair value of contingent consideration to change in the future, resulting in adjustments to the fair value of the Company’s contingent consideration liabilities, and the effect of any such adjustments could be material.

The following table represents a rollforward of the fair value of the Company’s contingent consideration liabilities:

~~Nine~~Three Months Ended ~~September 30, 2020~~March 31, 2021

(in thousands)

Balance at December 31, ~~2019~~2020

~~176,500~~189,600

~~Increase~~Decrease in fair value of contingent payments

~~12,600~~ (3,900)

Balance at ~~September 30, 2020~~March 31, 2021

~~189,100~~185,700

~~The “Increase in fair value of contingent payments” in the table above was primarily due to changes in market interest rates.~~

F.Marketable Securities and Equity Investments

A summary of the Company’s cash equivalents and marketable securities, which are recorded at fair value (and do not include ~~$2.2~~$2.4 billion and ~~$2.3~~$2.8 billion of cash as of ~~September 30, 2020~~March 31, 2021 and December 31, ~~2019,~~2020, respectively), is shown below:


		As of September 30, 2020								As of December 31, 2019									As of March 31, 2021								As of December 31, 2020
		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Fair Value		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Fair Value			Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Fair Value		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Fair Value
		(in thousands)																	(in thousands)
Cash equivalents:	Cash equivalents:																	Cash equivalents:
Money market funds	Money market funds	$	3,130,364	$	0	$	0	$	3,130,364	$	791,039	$	0	$	0	$	791,039	Money market funds	$	3,890,303	$	0	$	0	$	3,890,303	$	3,141,053	$	0	$	0	$	3,141,053
Corporate debt securities		0		0		0		0		6,070		0		0		6,070
Commercial paper		5,000		1		0		5,001		29,470		3		(1)		29,472
Total cash equivalents	Total cash equivalents	$	3,135,364	$	1	$	0	$	3,135,365	$	826,579	$	3	$	(1)	$	826,581	Total cash equivalents	$	3,890,303	$	0	$	0	$	3,890,303	$	3,141,053	$	0	$	0	$	3,141,053
Marketable securities:	Marketable securities:																	Marketable securities:
Government-sponsored enterprise securities	Government-sponsored enterprise securities	$	91,256	$	33	$	(6)	$	91,283	$	12,689	$	44	$	0	$	12,733	Government-sponsored enterprise securities	$	62,332	$	30	$	0	$	62,362	$	80,046	$	17	$	0	$	80,063
Corporate debt securities	Corporate debt securities	275,554		1,067		(11)		276,610		301,458		391		(50)		301,799		Corporate debt securities	155,636		126		(46)		155,716		231,263		377		(42)		231,598
Commercial paper	Commercial paper	112,159		242		(5)		112,396		102,240		121		(5)		102,356		Commercial paper	258,068		27		(21)		258,074		163,286		19		(37)		163,268
Total marketable debt securities	Total marketable debt securities	478,969		1,342		(22)		480,289		416,387		556		(55)		416,888		Total marketable debt securities	476,036		183		(67)		476,152		474,595		413		(79)		474,929
Corporate equity securities	Corporate equity securities	103,463		209,219		0		312,682		113,829		168,255		0		282,084		Corporate equity securities	51,427		92,059		0		143,486		51,427		144,354		0		195,781
Total marketable securities	Total marketable securities	$	582,432	$	210,561	$	(22)	$	792,971	$	530,216	$	168,811	$	(55)	$	698,972	Total marketable securities	$	527,463	$	92,242	$	(67)	$	619,638	$	526,022	$	144,767	$	(79)	$	670,710

Available-for-sale debt securities were classified on the Company's condensed consolidated balance sheets at fair value as follows:

As of September 30, 2020 As of December 31, 2019
(in thousands)
Cash and cash equivalents $ 3,135,365 $ 826,581
Marketable securities 480,289 416,888
Total $ 3,615,654 $ 1,243,469

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~~VERTEX PHARMACEUTICALS INCORPORATED~~

~~Notes to Condensed Consolidated Financial Statements~~

~~(unaudited)~~


	As of March 31, 2021		As of December 31, 2020
	(in thousands)
Cash and cash equivalents	$	3,890,303	$	3,141,053
Marketable securities	476,152		474,929
Total	$	4,366,455	$	3,615,982

Available-for-sale debt securities by contractual maturity were as follows:


		As of September 30, 2020		As of December 31, 2019			As of March 31, 2021		As of December 31, 2020
		(in thousands)					(in thousands)
Matures within one year	Matures within one year	$	3,514,474	$	1,137,942	Matures within one year	$	4,358,433	$	3,526,185
Matures after one year through five years	Matures after one year through five years	101,180		105,527		Matures after one year through five years	8,022		89,797
Total	Total	$	3,615,654	$	1,243,469	Total	$	4,366,455	$	3,615,982

The Company has a limited number of available-for-sale debt securities in insignificant loss positions as of ~~September 30, 2020,~~March 31, 2021, which it does not intend to sell and has concluded it will not be required to sell before recovery of the amortized costs

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements (unaudited)

for the investments at maturity. The Company did 0t record any charges for other-than-temporary declines in the fair value of available-for-sale debt securities or gross realized gains or losses in the three ~~and nine~~ months ended ~~September 30, 2020~~March 31, 2021 and ~~2019.~~

As of September 30, 2020 and December 31, 2019, the total fair value of the Company’s strategic investments in the common stock of publicly traded companies was $312.7 million and $282.1 million, respectively, and was classified as “Marketable securities” on its condensed consolidated balance sheets.2020.

The Company records changes in the fair value of its investments in corporate equity securities to “Other ~~income (expense),~~expense, net” on its condensed consolidated statements of operations. During the three ~~and nine~~ months ended ~~September 30,~~March 31, 2021 and 2020, the ~~Company recorded~~Company’s net unrealized ~~gains of $69.8 million and $102.3 million, respectively,~~losses on corporate equity securities held at the conclusion of each period were as ~~of September 30, 2020.~~ follows:


	Three Months Ended March 31,
		2021		2020
		(in thousands)
Net unrealized losses		$	(52,295)	$	(39,440)

During the three ~~and nine~~ months ended September 30, 2019, the Company recorded a net unrealized loss of $31.2 million and a net unrealized gain of $68.9 million, respectively, on corporate equity securities held as of September 30, 2019. During the nine months ended September 30,March 31, 2020, the Company received proceeds of ~~$149.6~~$72.0 million related to the sale of the common stock of publicly traded companies, which had a total original weighted-average cost basis of ~~$51.3~~$26.7 million. There were 0 sales of the common stock of publicly traded companies during the ~~nine~~three months ended ~~September 30, 2019.~~March 31, 2021.

As of ~~September 30, 2020,~~March 31, 2021, the carrying value of the Company’s equity investments without readily determinable fair values, which are recorded in “Other assets” on its condensed consolidated balance sheets, was $20.8 million.

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~~VERTEX PHARMACEUTICALS INCORPORATED~~

~~Notes to Condensed Consolidated Financial Statements~~

~~(unaudited)~~

G.Accumulated Other Comprehensive Income (Loss)

The following table summarizes the changes in accumulated other comprehensive income (loss) by component:

Unrealized Holding Gains (Losses), Net of Tax
Foreign Currency Translation Adjustment On Available-For-Sale Debt Securities On Foreign Currency Forward Contracts Total
(in thousands)
Balance at December 31, 2019 $ (895) $ 503 $ (1,581) $ (1,973)
Other comprehensive (loss) income before reclassifications (12,616) 818 (20,913) (32,711)
Amounts reclassified from accumulated other comprehensive loss 0 0 (6,298) (6,298)
Net current period other comprehensive (loss) income (12,616) 818 (27,211) (39,009)
Balance at September 30, 2020 $ (13,511) $ 1,321 $ (28,792) $ (40,982)
Balance at December 31, 2018 $ (11,227) $ (536) $ 12,422 $ 659
Other comprehensive income before reclassifications 10,263 1,111 26,663 38,037
Amounts reclassified from accumulated other comprehensive income 0 0 (19,849) (19,849)
Net current period other comprehensive income 10,263 1,111 6,814 18,188
Balance at September 30, 2019 $ (964) $ 575 $ 19,236 $ 18,847


	Foreign Currency Translation Adjustment		Unrealized Holding Gains (Losses), Net of Tax				Total
			On Available-For-Sale Debt Securities		On Foreign Currency Forward Contracts
	(in thousands)
Balance at December 31, 2020	$	(15,678)	$	334	$	(53,136)	$	(68,480)
Other comprehensive income (loss) before reclassifications	1,430		(218)		21,019		22,231
Amounts reclassified from accumulated other comprehensive income (loss)	0		0		12,947		12,947
Net current period other comprehensive income (loss)	1,430		(218)		33,966		35,178
Balance at March 31, 2021	$	(14,248)	$	116	$	(19,170)	$	(33,302)

Balance at December 31, 2019	$	(895)	$	503	$	(1,581)	$	(1,973)
Other comprehensive (loss) income before reclassifications	(2,662)		(764)		25,772		22,346
Amounts reclassified from accumulated other comprehensive income (loss)	0		0		(6,990)		(6,990)
Net current period other comprehensive (loss) income	(2,662)		(764)		18,782		15,356
Balance at March 31, 2020	$	(3,557)	$	(261)	$	17,201	$	13,383

H.Hedging

Foreign currency forward contracts - Designated as hedging instruments

The Company maintains a hedging program intended to mitigate the effect of changes in foreign exchange rates for a portion of the Company’s forecasted product revenues denominated in certain foreign currencies. The program includes foreign currency forward contracts that are designated as cash flow hedges under U.S. GAAP having contractual durations from one to eighteen months. The Company recognizes realized gains and losses for the effective portion of such contracts in “Product revenues, net” in its condensed consolidated statements of operations in the same period that it recognizes the product revenues that were impacted by the hedged foreign exchange rate changes.

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements (unaudited)

The Company formally documents the relationship between foreign currency forward contracts (hedging instruments) and forecasted product revenues (hedged items), as well as the Company’s risk management objective and strategy for undertaking various hedging activities, which includes matching all foreign currency forward contracts that are designated as cash flow hedges to forecasted transactions. The Company also formally assesses, both at the hedge’s inception and on an ongoing basis, whether the foreign currency forward contracts are highly effective in offsetting changes in cash flows of hedged items on a prospective and retrospective basis. If the Company were to determine that a (i) foreign currency forward contract is not highly effective as a cash flow hedge, (ii) foreign currency forward contract has ceased to be a highly effective hedge or (iii) forecasted transaction is no longer probable of occurring, the Company would discontinue hedge accounting treatment prospectively. The Company measures effectiveness based on the change in fair value of the forward contracts and the fair value of the hypothetical foreign currency forward contracts with terms that match the critical terms of the risk being hedged. As of ~~September 30, 2020,~~March 31, 2021, all hedges were determined to be highly effective.

The Company considers the impact of its counterparties’ credit risk on the fair value of the foreign currency forward contracts. As of ~~September 30, 2020~~March 31, 2021 and December 31, ~~2019,~~2020, credit risk did not change the fair value of the Company’s foreign currency forward contracts.

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~~VERTEX PHARMACEUTICALS INCORPORATED~~

~~Notes to Condensed Consolidated Financial Statements~~

~~(unaudited)~~

The following table summarizes the notional amount in U.S. dollars of the Company’s outstanding foreign currency forward contracts designated as cash flow hedges under U.S. GAAP:


		As of September 30, 2020		As of December 31, 2019			As of March 31, 2021		As of December 31, 2020
Foreign Currency	Foreign Currency	(in thousands)				Foreign Currency	(in thousands)
Euro	Euro	$	632,621	$	501,197	Euro	$	892,995	$	745,099
British pound sterling	British pound sterling	166,707		87,032		British pound sterling	250,528		160,427
Australian dollar	Australian dollar	92,524		89,705		Australian dollar	100,733		99,922
Canadian dollar	Canadian dollar	74,749		50,452		Canadian dollar	80,122		86,468
Total foreign currency forward contracts	Total foreign currency forward contracts	$	966,601	$	728,386	Total foreign currency forward contracts	$	1,324,378	$	1,091,916

Foreign currency forward contracts - Not designated as hedging instruments

The Company also enters into foreign currency forward contracts with contractual maturities of less than one month, ~~that~~which are designed to mitigate the effect of changes in foreign exchange rates on monetary assets and liabilities, including intercompany balances. These contracts are not designated as hedging instruments under U.S. GAAP. The Company recognizes realized gains and losses for such contracts in “Other ~~income (expense),~~expense, net” in its condensed consolidated statements of operations each period. As of ~~September 30, 2020,~~March 31, 2021, the notional amount of the Company’s outstanding foreign currency forward contracts where hedge accounting under U.S. GAAP is not applied was ~~$609.9~~$386.7 million.

During the three ~~and nine~~ months ended ~~September 30,~~March 31, 2021 and 2020, ~~and 2019,~~ the Company recognized the following related to foreign currency forward contacts in its condensed consolidated statements of operations:


		Three Months Ended September 30,				Nine Months Ended September 30,					Three Months Ended March 31,
		2020		2019		2020		2019				2021		2020
		(in thousands)										(in thousands)
Designated as hedging instruments - Reclassified from AOCI	Designated as hedging instruments - Reclassified from AOCI									Designated as hedging instruments - Reclassified from AOCI
Product revenues, net	Product revenues, net	$	(7,249)	$	10,304	$	8,039	$	25,381	Product revenues, net		$	(16,518)	$	8,922
Not designated as hedging instruments	Not designated as hedging instruments									Not designated as hedging instruments
Other income (expense), net		$	25,897	$	(8,812)	$	15,724	$	(10,874)
Other expense, net										Other expense, net		$	(7,997)	$	(16,229)

Total reported in the Condensed Consolidated Statement of Operations	Total reported in the Condensed Consolidated Statement of Operations									Total reported in the Condensed Consolidated Statement of Operations
Product revenues, net	Product revenues, net	$	1,536,271	$	949,828	$	4,575,863	$	2,747,461	Product revenues, net		$	1,723,305	$	1,515,107
Other income (expense), net		$	84,386	$	(31,747)	$	139,621	$	64,802
Other expense, net										Other expense, net		$	(52,653)	$	(61,130)

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements (unaudited)

The following table summarizes the fair value of the Company’s outstanding foreign currency forward contracts designated as cash flow hedges under U.S. GAAP included on its condensed consolidated balance sheets:

As of September 30, 2020

As of March 31, 2021

Assets

Liabilities

Assets

Liabilities

Classification

Fair Value

Classification

Fair Value

Classification

Fair Value

Classification

Fair Value

(in thousands)

Prepaid expenses and other current assets

673

Other current liabilities

(29,554)

Prepaid expenses and other current assets

7,039

Other current liabilities

(28,743)

Other assets

Other long-term liabilities

(3,254)

Other assets

1,944

Other long-term liabilities

(433)

Total assets

673

Total liabilities

(32,808)

Total assets

8,983

Total liabilities

(29,176)

As of December 31, 2019
Assets Liabilities
Classification Fair Value Classification Fair Value
(in thousands)
Prepaid expenses and other current assets $ 9,725 Other current liabilities $ (5,533)
Other assets 0 Other long-term liabilities (1,821)
Total assets $ 9,725 Total liabilities $ (7,354)

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~~VERTEX PHARMACEUTICALS INCORPORATED~~

~~Notes to Condensed Consolidated Financial Statements~~

~~(unaudited)~~


As of December 31, 2020
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid expenses and other current assets	$	0	Other current liabilities	$	(59,184)
Other assets	0		Other long-term liabilities	(4,283)
Total assets	$	0	Total liabilities	$	(63,467)

As of ~~September 30, 2020,~~March 31, 2021, the Company expects the amounts that are related to foreign exchange forward contracts designated as cash flow hedges under U.S. GAAP recorded in “Prepaid expenses and other current assets” and “Other current liabilities” to be reclassified to earnings within twelve months.

The following table summarizes the potential effect of offsetting derivatives by type of financial instrument designated as cash flow hedges under U.S. GAAP on the Company’s condensed consolidated balance sheets:


		As of September 30, 2020											As of March 31, 2021
		Gross Amounts Recognized		Gross Amounts Offset		Gross Amounts Presented		Gross Amounts Not Offset		Legal Offset			Gross Amounts Recognized		Gross Amounts Offset		Gross Amounts Presented		Gross Amounts Not Offset		Legal Offset
Foreign currency forward contracts	Foreign currency forward contracts	(in thousands)										Foreign currency forward contracts	(in thousands)
Total assets	Total assets	$	673	$	0	$	673	$	(673)	$	0	Total assets	$	8,983	$	0	$	8,983	$	(8,983)	$	0
Total liabilities	Total liabilities	(32,808)		0		(32,808)		673		(32,135)		Total liabilities	(29,176)		0		(29,176)		8,983		(20,193)


		As of December 31, 2019											As of December 31, 2020
		Gross Amounts Recognized		Gross Amounts Offset		Gross Amounts Presented		Gross Amounts Not Offset		Legal Offset			Gross Amounts Recognized		Gross Amounts Offset		Gross Amounts Presented		Gross Amounts Not Offset		Legal Offset
Foreign currency forward contracts	Foreign currency forward contracts	(in thousands)										Foreign currency forward contracts	(in thousands)
Total assets	Total assets	$	9,725	$	0	$	9,725	$	(7,354)	$	2,371	Total assets	$	0	$	0	$	0	$	0	$	0
Total liabilities	Total liabilities	(7,354)		0		(7,354)		7,354		0		Total liabilities	(63,467)		0		(63,467)		0		(63,467)

I.Inventories

Inventories consisted of the following:


		As of September 30, 2020		As of December 31, 2019			As of March 31, 2021		As of December 31, 2020
		(in thousands)					(in thousands)
Raw materials	Raw materials	$	42,542	$	26,247	Raw materials	$	44,921	$	46,232
Work-in-process	Work-in-process	135,220		107,021		Work-in-process	170,721		161,324
Finished goods	Finished goods	67,698		34,234		Finished goods	83,221		73,221
Total	Total	$	245,460	$	167,502	Total	$	298,863	$	280,777

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Notes to Condensed Consolidated Financial Statements

(unaudited)

J.Stock-based Compensation Expense and Share Repurchase Programs

Stock-based compensation expense

During the three ~~and nine~~ months ended ~~September 30,~~March 31, 2021 and 2020, ~~and 2019,~~ the Company recognized the following stock-based compensation expense:

Three Months Ended September 30, Nine Months Ended September 30,
2020 2019 2020 2019
(in thousands)
Stock-based compensation expense by type of award:
Restricted stock and restricted stock units (including PSUs) $ 84,043 $ 61,175 $ 279,611 $ 185,651
Stock options 13,221 21,737 47,334 76,053
ESPP share issuances 3,225 3,044 8,565 8,430
Stock-based compensation expense related to inventories (950) (536) (3,076) (1,236)
Total stock-based compensation expense included in costs and expenses $ 99,539 $ 85,420 $ 332,434 $ 268,898
Stock-based compensation expense by line item:
Cost of sales $ 1,250 $ 1,337 $ 3,998 $ 4,178
Research and development expenses 60,770 52,504 203,732 167,851
Sales, general and administrative expenses 37,519 31,579 124,704 96,869
Total stock-based compensation expense included in costs and expenses 99,539 85,420 332,434 268,898
Income tax effect (35,295) (21,996) (130,692) (87,638)
Total stock-based compensation expense, net of tax $ 64,244 $ 63,424 $ 201,742 $ 181,260

The following table sets forth the Company’s unrecognized stock-based compensation expense as of September 30, 2020, by type of award and the weighted-average period over which that expense is expected to be recognized:

As of September 30, 2020
Unrecognized Expense Weighted-average
Recognition Period
(in thousands) (in years)
Type of award:
Restricted stock units (including PSUs) $ 487,254 2.06
Stock options $ 76,261 1.95
ESPP share issuances $ 3,265 0.44

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~~VERTEX PHARMACEUTICALS INCORPORATED~~

~~Notes to Condensed Consolidated Financial Statements~~

~~(unaudited)~~

~~The following table summarizes information about stock options outstanding and exercisable as of September 30, 2020:~~

Options Outstanding Options Exercisable
Range of
Exercise Prices
Number
Outstanding Weighted-average
Remaining
Contractual Life Weighted-average
Exercise Price Number
Exercisable Weighted-average
Exercise Price
(in thousands) (in years) (per share) (in thousands) (per share)
$36.28–$40.00 62 1.09 $ 38.06 62 $ 38.06
$40.01–$60.00 157 1.98 $ 47.13 157 $ 47.13
$60.01–$80.00 105 3.49 $ 74.82 104 $ 74.82
$80.01–$100.00 1,029 5.66 $ 88.91 919 $ 89.20
$100.01–$120.00 129 4.39 $ 109.27 128 $ 109.21
$120.01–$140.00 282 4.98 $ 129.42 281 $ 129.43
$140.01–$160.00 740 7.36 $ 155.49 369 $ 155.41
$160.01–$180.00 599 7.76 $ 168.34 282 $ 165.74
$180.01–$200.00 1,252 8.14 $ 185.31 422 $ 184.85
$200.01–$286.27 23 9.67 $ 286.27 23 $ 286.27
Total 4,378 6.63 $ 140.26 2,747 $ 123.22


	Three Months Ended March 31,
		2021		2020
		(in thousands)
Stock-based compensation expense by type of award:
Restricted stock units (including PSUs) and restricted stock		$	100,826	$	97,149
Stock options		10,596		17,266
ESPP share issuances		5,615		2,485
Stock-based compensation expense related to inventories		(1,863)		(1,194)
Total stock-based compensation expense included in costs and expenses		$	115,174	$	115,706

Stock-based compensation expense by line item:
Cost of sales		$	1,431	$	1,361
Research and development expenses		72,802		72,687
Sales, general and administrative expenses		40,941		41,658
Total stock-based compensation expense included in costs and expenses		115,174		115,706
Income tax effect		(31,251)		(64,246)
Total stock-based compensation expense, net of tax		$	83,923	$	51,460

Share repurchase programs

In ~~2018,~~2019, the Company’s Board of Directors approved a share repurchase program (the ~~“2018~~“2019 Share Repurchase Program”), pursuant to which the Company repurchased $500.0 million of its common stock in ~~2018~~2019 and ~~2019.~~2020. During the ~~nine~~three months ended ~~September 30, 2019,~~March 31, 2020, the Company repurchased ~~832,186~~1,403,868 shares of its common stock under the ~~2018~~2019 Share Repurchase Program for an aggregate of ~~$150.0~~$300.0 million.

In November 2020, the Company’s Board of Directors approved a new share repurchase program (the “2020 Share Repurchase Program”), pursuant to which the Company was authorized to repurchase up to $500.0 million ~~including commissions and fees.~~of its common stock by December 31, 2022. During the three months ended March 31, 2021, the Company repurchased 1,988,941 shares of its common stock under the 2020 Share Repurchase Program for an aggregate of $424.9 million. As of ~~June 30, 2019,~~March 31, 2021, the Company had repurchased the entire $500.0 million it was authorized to repurchase of its common stock under the ~~2018~~2020 Share Repurchase Program.

In 2019, the Company’s Board of Directors approved a new share repurchase program (the “2019 Share Repurchase Program”), pursuant to which the Company is authorized to repurchase up to $500.0 million of its common stock between August 1, 2019 and December 31, 2020. During the nine months ended September 30, 2020, the Company repurchased 1,806,587 shares of its common stock under the 2019 Share Repurchase Program for an aggregate of $408.0 million including commissions and fees. As of September 30, 2020, there was a total of $56.0 million remaining for repurchases under the 2019 Share Repurchase Program. The Company expects to fund further repurchases of its common stock through a combination of cash on hand and cash generated by operations.

Under the 2019 Share Repurchase Program, the Company is authorized to purchase shares from time to time through open market or privately negotiated transactions. Such purchases are made pursuant to Rule 10b5-1 plans or other means as determined by the Company’s management and in accordance with the requirements of the SEC.

K.Income Taxes

The Company is subject to U.S. federal, state, and foreign income taxes. For the three ~~and nine~~ months ended ~~September 30,~~March 31, 2021 and 2020, the Company recorded provisions for income taxes of ~~$78.4~~$167.8 million and ~~$120.7 million, respectively. For the three and nine months ended September 30, 2019, the Company recorded provisions for income taxes of $13.1 million and $124.4~~$54.8 million, respectively.

The Company’s effective tax rate ~~for the third quarter~~ of 2020 was lower than the U.S. statutory rate primarily due to a discrete tax benefit associated with an increase in the United Kingdom’s corporate tax rate. The Company’s effective tax rate for the nine months ended September 30, 2020 was also lower than the U.S. statutory rate due to discrete tax benefits associated with an intra-entity transfer of intellectual property rights to the United Kingdom and the write-off of a long-term intercompany receivable as well as excess tax benefits related to stock-based compensation. The Company’s effective tax rate

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~~VERTEX PHARMACEUTICALS INCORPORATED~~

~~Notes to Condensed Consolidated Financial Statements~~

~~(unaudited)~~

20% for the three ~~and nine~~ months ended ~~September 30, 2019~~March 31, 2021 was lower than the U.S. statutory rate primarily due to excess tax benefits related to stock-based compensation.

~~In the second quarter of 2020, the Company completed an intra-entity transfer of intellectual property rights to the United Kingdom, resulting in a deferred tax benefit of $209.0 million.~~ The ~~Company expects to be able to utilize the deferred tax asset resulting from the intra-entity transfer.~~

The Company released its valuation allowance on the majority of its net operating losses and other deferred tax assets as of December 31, 2018. Starting in 2019, the Company began recording a provision for income taxes on its pre-tax income using anCompany’s effective tax rate ~~approximating~~of 8% for the three months ended March 31, 2020 was lower than the U.S. statutory ~~rates. The Company expects~~rate primarily due to ~~utilize its remaining previously benefited U.S. net operating losses in 2020. As~~ a ~~result,~~discrete benefit related to the write-off of a ~~larger portion of the Company’s~~long-term intercompany receivable and excess tax ~~provision will represent a cash tax payable in future periods.~~benefits related to stock-based compensation.

~~The Company maintained a valuation allowance of $205.2 million related primarily to U.S. state and foreign tax attributes as of December 31, 2019.~~ On a periodic basis, the Company reassesses any valuation allowances that it maintains on its deferred tax assets, weighing positive and negative evidence to assess the recoverability of the deferred tax assets.

~~In March~~ As of December 31, 2020, the ~~Coronavirus Aid, Relief,~~Company maintained a valuation allowance of $213.8 million related primarily to U.S. state and ~~Economic Security~~foreign tax attributes.

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements (unaudited)

As part of the Tax Cut and Jobs Act ~~(the “CARES Act”~~of 2017, the Company is subject to a territorial tax system in which the requirement is to establish an accounting policy in providing for tax on Global Intangible Low Taxed Income (“GILTI”) ~~was signed into law. The CARES Act includes provisions relating to several aspects of corporate income taxes.~~earned by certain foreign subsidiaries. The Company ~~does not currently expect~~has elected to treat the ~~CARES Act to have~~impact of GILTI as a ~~significant impact on~~current tax expense in its provision for income ~~taxes; however, it will continue to monitor the provisions of the CARES Act in relation to its operations.~~taxes.

The Company has reviewed the tax positions taken, or to be taken, in its tax returns for all tax years currently open to examination by a taxing authority. Unrecognized tax benefits represent the aggregate tax effect of differences between tax return positions and the benefits recognized in the consolidated financial statements. As of ~~September 30, 2020~~March 31, 2021 and December 31, ~~2019,~~2020, the Company had ~~$73.8~~$81.8 million and ~~$33.9~~$75.8 million, respectively, of ~~gross~~net unrecognized tax benefits, which would affect the Company’s tax rate if recognized. The Company does not expect that its unrecognized tax benefits will materially change within the next twelve months. The Company accrues interest and penalties related to unrecognized tax benefits as a component of its provision for income taxes. The Company did not recognize any material interest or penalties related to uncertain tax positions during the three ~~and nine~~ months ended ~~September 30, 2020~~March 31, 2021 and ~~2019.~~2020.

As of ~~September 30, 2020,~~March 31, 2021, foreign earnings, which were not significant, have been retained by foreign subsidiaries for indefinite reinvestment. Upon repatriation of those earnings, in the form of dividends or otherwise, the Company could be subject to withholding taxes payable to the various foreign countries.

The Company files U.S. federal income tax returns and income tax returns in various state, local and foreign jurisdictions. The Company is no longer subject to any tax assessment from an income tax examination in the U.S. or any other major taxing jurisdiction for years before 2011, except where the Company has net operating losses or tax credit carryforwards that originate before 2011. The Company has various income tax audits ongoing at any time throughout the world.

L.Commitments and Contingencies

Revolving Credit Facilities

The Company and certain of its subsidiaries have entered into 2 ~~Credit Agreements~~credit agreements (the “Credit Agreements”) with Bank of America, N.A., as administrative agent and the lenders referred to therein (the “Lenders”). The Credit Agreements were not drawn upon at closing and the Company has not drawn upon them to date. Amounts drawn pursuant to the Credit Agreements, if any, will be used for general corporate purposes. Any amounts borrowed under the Credit Agreements will bear interest, at the Company’s option, at either a base rate or a Eurocurrency rate, in each case plus an applicable margin based on the Company’s consolidated leverage ratio (the ratio of the Company’s total consolidated funded indebtedness to the Company’s consolidated EBITDA for the most recently completed four fiscal quarter period).

In September 2019, the Company and certain of its subsidiaries entered into a $500.0 million unsecured revolving facility (the “2019 Credit Agreement”) with the Lenders, which matures on September 17, 2024. ~~The 2019 Credit Agreement~~

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~~VERTEX PHARMACEUTICALS INCORPORATED~~

~~Notes to Condensed Consolidated Financial Statements~~

~~(unaudited)~~

~~superseded the Company’s credit agreement entered into in 2016 with Bank of America, N.A serving in the same capacity.~~ Under the 2019 Credit Agreement, the applicable margins on base rate loans range from 0.125% to 0.500% and the applicable margins on Eurocurrency loans range from 1.125% to 1.500%. The 2019 Credit Agreement provides a sublimit of $50.0 million for letters of credit.

In September 2020, the Company and certain of its subsidiaries entered into a $2.0 billion unsecured revolving facility (the “2020 Credit Agreement”) with the Lenders, which matures on September 18, 2022. Under the 2020 Credit Agreement, the applicable margins on base rate loans range from 0.500% to 0.875% and the applicable margins on Eurocurrency loans range from 1.500% to 1.875%. The 2020 Credit Agreement does not ~~include a sublimit for~~support letters of credit.

Subject to satisfaction of certain conditions, the Company may request that the borrowing capacity for each of the Credit Agreements be increased by an additional $500.0 million. Any amounts borrowed pursuant to the Credit Agreements are guaranteed by certain of the Company’s existing and future domestic subsidiaries, subject to certain exceptions.

The Credit Agreements contain customary representations and warranties and affirmative and negative covenants, including financial covenants to maintain (x) subject to certain limited exceptions, a consolidated leverage ratio of 3.50 to 1.00, subject to an increase to 4.00 to 1.00 following a material acquisition and (y) a consolidated interest coverage ratio of

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements (unaudited)

2.50 to 1.00, in each case measured on a quarterly basis. As of ~~September 30, 2020,~~March 31, 2021, the Company was in compliance with the covenants described above. The Credit Agreements also contain customary events of default. In the case of a continuing event of default, the administrative agent would be entitled to exercise various remedies, including the acceleration of amounts due under outstanding loans.

Direct costs related to the Credit Agreements, which were not material to the Company’s financial statements, were deferred and recorded over the term of the Credit Agreements.

Guaranties and Indemnifications

As permitted under Massachusetts law, the Company’s Articles of Organization and By-laws provide that the Company will indemnify certain of its officers and directors for certain claims asserted against them in connection with their service as an officer or director. The maximum potential amount of future payments that the Company could be required to make under these indemnification provisions is unlimited. However, the Company has purchased directors’ and officers’ liability insurance policies that could reduce its monetary exposure and enable it to recover a portion of any future amounts paid. NaN indemnification claims currently are outstanding, and the Company believes the estimated fair value of these indemnification arrangements is minimal.

The Company customarily agrees in the ordinary course of its business to indemnification provisions in agreements with clinical trial investigators and sites in its drug development programs, sponsored research agreements with academic and not-for-profit institutions, various comparable agreements involving parties performing services for the Company and its real estate leases. The Company also customarily agrees to certain indemnification provisions in its drug discovery, development and commercialization collaboration agreements. With respect to the Company’s clinical trials and sponsored research agreements, these indemnification provisions typically apply to any claim asserted against the investigator or the investigator’s institution relating to personal injury or property damage, violations of law or certain breaches of the Company’s contractual obligations arising out of the research or clinical testing of the Company’s compounds or drug candidates. With respect to lease agreements, the indemnification provisions typically apply to claims asserted against the landlord relating to personal injury or property damage caused by the Company, to violations of law by the Company or to certain breaches of the Company’s contractual obligations. The indemnification provisions appearing in the Company’s collaboration agreements are similar to those for the other agreements discussed above, but in addition provide some limited indemnification for its collaborator in the event of third-party claims alleging infringement of intellectual property rights. In each of the cases above, the indemnification obligation generally survives the termination of the agreement for some extended period, although the Company believes the obligation typically has the most relevance during the contract term and for a short period of time thereafter. The maximum potential amount of future payments that the Company could be required to make under these provisions is generally unlimited. The Company has purchased insurance policies covering personal injury, property damage and general liability that reduce its exposure for indemnification and would enable it in many cases to recover all or a portion of any future amounts paid. The Company has never paid any material amounts to defend lawsuits

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~~VERTEX PHARMACEUTICALS INCORPORATED~~

~~Notes to Condensed Consolidated Financial Statements~~

~~(unaudited)~~

or settle claims related to these indemnification provisions. Accordingly, the Company believes the estimated fair value of these indemnification arrangements is minimal.

Other Contingencies

The Company has certain contingent liabilities that arise in the ordinary course of its business activities. The Company accrues a reserve for contingent liabilities when it is probable that future expenditures will be made, and such expenditures can be reasonably estimated. There were 0 material contingent liabilities accrued as of ~~September 30, 2020~~March 31, 2021 or December 31, ~~2019.~~2020.

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements (unaudited)

M.Additional Cash Flow Information

The cash, cash equivalents and restricted cash at the beginning and ending of each period presented in the Company’s condensed consolidated statements of cash flows consisted of the following:

Nine Months Ended September 30,
2020 2019
Beginning of period End of period Beginning of period End of period
(in thousands)
Cash and cash equivalents $ 3,109,322 $ 5,358,087 $ 2,650,134 $ 3,397,941
Prepaid expenses and other current assets 8,004 2,898 4,910 6,650
Other assets 3,355 0 3,209 0
Cash, cash equivalents and restricted cash per statement of cash flows $ 3,120,681 $ 5,360,985 $ 2,658,253 $ 3,404,591

N.~~Facilities~~

~~Cell and Genetic Therapies Lease~~

In 2019, the Company entered into an agreement to lease approximately 269,000 square feet of office and laboratory space near its corporate headquarters in Boston, MA. The lease agreement includes an initial term of 15 years plus a period to install leasehold improvements, with an option to extend the lease term for up to 2 additional ten-year periods. The Company expects base rent payments to commence in the fourth quarter of 2021. The Company has utilized the initial period, which commenced in the third quarter of 2020 upon occupation of the building, as its lease term. As of September 30, 2020, the Company recorded a right-of-use asset of $256.8 million and an operating lease liability of $268.5 million related to the lease agreement on its condensed consolidated balance sheet.

~~Boston Continuous Manufacturing Facility~~

In the third quarter of 2020, the Company purchased its continuous manufacturing facility located near its corporate headquarters in Boston, MA from its former landlord for $155.3 million in cash. As of September 30, 2020, the Company adjusted its condensed consolidated balance sheet to (i) classify the building within “Property and equipment, net” with a 40 years useful life, (ii) derecognize a previously recorded right-of-use asset and operating lease liability for the facility and (iii) record a finance lease for the land on which the facility is constructed. The previously recognized right-of-use asset and operating lease liability and the newly recognized finance lease related to the land were not significant to the Company’s condensed consolidated balance sheet for the periods presented.


	Three Months Ended March 31,
	2021				2020
	Beginning of period		End of period		Beginning of period		End of period
	(in thousands)
Cash and cash equivalents	$	5,988,187	$	6,304,330	$	3,109,322	$	3,593,412
Prepaid expenses and other current assets	658		8,577		8,004		8,552
Other assets	0		0		3,355		0
Cash, cash equivalents and restricted cash per condensed consolidated statement of cash flows	$	5,988,845	$	6,312,907	$	3,120,681	$	3,601,964

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VERTEX PHARMACEUTICALS INCORPORATED

Notes to Condensed Consolidated Financial Statements (unaudited)

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Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

OVERVIEW

We invest in scientific innovation to create transformative medicines for people with serious diseases with a focus on specialty markets. We have four approved medicines to treat cystic fibrosis, or CF, a life-threatening genetic disease, and are focused on ~~expanding~~increasing the number of people with CF eligible ~~for~~and able to receive our ~~medicines.~~current medicines through label expansions, approval of new medicines and expanded reimbursement. We are broadening our pipeline into additional disease areas through internal research efforts and accessing external innovation through business development transactions.

~~In October 2019, TRIKAFTA (elexacaftor/tezacaftor/ivacaftor and ivacaftor), our~~Our triple combination regimen, TRIKAFTA/KAFTRIO, was approved ~~by the U.S. Food and Drug Administration, or FDA, for the treatment of people with CF 12 years of age and older who have at least one~~ ~~F508del~~ ~~mutation~~in 2019 in the ~~cystic fibrosis transmembrane conductance regulator,~~United States, or ~~CFTR, gene. In August~~U.S., and in 2020~~our~~ triple combination regimen was approved by the European Commission for people with CF 12 years of age and older with specific mutations in their CFTR gene. We market our triple combination regimen as KAFTRIO in the European Union, or E.U. Approval of TRIKAFTA and KAFTRIO increased the number of people with CF that are eligible for our medicines by up to 16,000 and provides an additional treatment option for many people who are eligible for one of our previously approved products. Collectively, our four medicines ~~currently~~ are approved to treat the majority of the approximately 83,000 people with CF in North America, Europe and Australia. We are evaluating our ~~triple combination regimen~~medicines in additional patient populations, including younger children, with the goal of having small molecule treatments for up to 90% of people with CF. We are also pursuing genetic therapies to address the remaining 10% of people with CF.

Beyond CF, ~~our~~we continue to research and develop small molecule ~~programs include programs focused on developing treatments~~drug candidates for the treatment of serious diseases, including alpha-1 antitrypsin, or AAT, deficiency, APOL1-mediated kidney diseases and pain. We are also focused on developing cell and genetic therapies for various diseases in our pipeline, including sickle cell disease, or SCD, beta thalassemia, type 1 diabetes, or T1D, Duchenne muscular dystrophy, or DMD, myotonic dystrophy, or DM1, and CF. We are evaluating CTX001, a genetic therapy, as a potential treatment for ~~sickle cell disease, or~~ SCD and transfusion-dependent beta thalassemia, or TDT, the most severe form of beta thalassemia, in Phase 1/2 clinical trials in collaboration with CRISPR Therapeutics AG, or CRISPR. In ~~2019, through a series of strategic transactions,~~T1D, we ~~acquired preclinical programs to develop cell-based therapies for type 1 diabetes, or T1D, and preclinical genetic therapy~~are pursuing two programs for ~~Duchenne muscular dystrophy, or DMD,~~the transplant of functional islets into patients: transplantation of islet cells alone, using immunosuppression to protect the implanted cells, and ~~myotonic dystrophy type 1, or DM1.~~implantation of the islet cells inside a novel immunoprotective device.

Financial Highlights

Revenues

In the ~~third~~first quarter of ~~2020,~~2021, our net product revenues continued to increase due to the ~~approval~~uptake of KAFTRIO in Europe and continued performance of TRIKAFTA in ~~late 2019 and uptake of our medicines in ex-U.S. markets following completion of several significant reimbursement agreements.~~the U.S.

Expenses

Our ~~combined~~total R&D and SG&A expenses ~~decreased~~increased to ~~$678.0~~$648.1 million in the ~~third~~first quarter of ~~2020 from $715.6~~2021 as compared to $630.8 million in the ~~third~~first quarter of ~~2019.~~2020. In the ~~third~~first quarter of ~~2020,~~2021, cost of sales was ~~12%~~approximately 11% of our net product revenues.

~~Balance Sheet~~

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Business Updates

Cystic Fibrosis

~~TRIKAFTA/KAFTRIO~~We expect to continue to grow our CF business by increasing the number of people with CF eligible and able to receive our medicines.

Since the beginning of 2021, we have made the following progress with respect to our CF business.

•The Australian Therapeutic Goods Administration approved the use of TRIKAFTA (elexacaftor/tezacaftor/ivacaftor and ivacaftor)

•~~In August 2020, the European Commission granted marketing authorization~~ for ~~KAFTRIO to treat~~ people with CF 12 years of age and older ~~with~~who have at least one F508del ~~mutation and one minimal function mutation, or two~~ ~~F508del~~ ~~mutations.~~ mutation.

•~~The~~We filed our post-marketing application with the European Medicines Agency, or EMA, ~~validated a Type II Variation Marketing Authorization Application, or MAA,~~ for the expanded indication of KAFTRIO ~~that we believe supports an expansion of the E.U. label~~ (elexacaftor/tezacaftor/ivacaftor and ivacaftor)to ~~people~~include children with CF ~~who have one copy of the~~ ~~F508del~~ ~~mutation.~~

•~~We reported positive data from our Phase 3 clinical trial evaluating the use of our triple combination regimen in children~~ 6 to 11 years of ~~age with CF who have two copies of the~~ ~~F508del~~ ~~mutation or who have one~~ ~~F508del~~ ~~mutation and one minimal function mutation. We plan to submit a supplemental New Drug Application, or sNDA, to the FDA for children 6 to 11 years of age with at least one~~ ~~F508del~~ ~~mutation in the fourth quarter of 2020.~~age.

•~~The FDA accepted three sNDAs for TRIKAFTA, SYMDEKO~~TRIKAFTA/KAFTRIO is now approved and ~~KALYDECO. These regulatory submissions are intended~~reimbursed or accessible in 12 countries outside the U.S., including Denmark, Germany, Ireland, Israel, Switzerland and the countries within the UK.

Pipeline

We continue to ~~expand the labels~~advance a pipeline of ~~TRIKAFTA, SYMDEKO~~potentially transformative small molecule, cell and ~~KALYDECO to include people with CF who have rare CFTR mutations.~~

•~~We are initiating a Phase 3 clinical trial evaluating the use of our triple combination regimen in children two to five years of age with CF who have either two copies of the~~ ~~F508del~~ ~~mutation or one copy of the~~ ~~F508del~~ ~~mutation and one minimal function mutation.~~

~~SYMDEKO/SYMKEVI (tezacaftor and ivacaftor)~~

•~~The EMA’s Committee for Medicinal Products for Human Use, or CHMP, adopted a positive opinion for the label extension of SYMKEVI for the treatment of children 6 to 11 years of age with CF with two~~ ~~F508del~~ ~~mutations or one~~ ~~F508del~~ ~~mutation and certain residual function mutations~~.

~~KALYDECO (ivacaftor)~~

•In September 2020, the FDA approved KALYDECO to treat infants with CF four months of age to less than six months of age who have at least one mutation in their CFTR gene that is responsive to KALYDECO.

•The EMA’s CHMP adopted a positive opinion for the label extension of KALYDECO for the treatment of infants with CF four months of age to less than six months of age who have at least one mutation in their CFTR gene that is responsive to KALYDECO.

~~Genetic Therapies~~

•~~We entered into a new collaboration with Moderna, Inc., or Moderna,~~genetic therapies aimed at serious diseases. Since the ~~discovery and development~~beginning of ~~lipid nanoparticles and mRNAs that can deliver gene-editing therapies to lung cells for~~2021, we have made the ~~treatment of CF.~~

~~Pipeline~~following progress in activities supporting these efforts.

Beta Thalassemia and Sickle Cell Disease

•We and our collaborator, CRISPR, are evaluating the use of ~~an ex-vivo~~a non-viral ex vivo CRISPR gene-editing therapy for the treatment of TDT and SCD. This approach aims to edit a ~~patient’s~~person’s hematopoietic stem cells to produce fetal hemoglobin in red blood cells, which has the potential to reduce or eliminate symptoms associated with ~~disease.~~the diseases.

•We and our collaborator, CRISPR, previously announced that, as of June 2020, seven patients had been dosed across the two Phase 1/2 clinical trials of the investigational CRISPR/Cas9 gene-editing therapy CTX001 and presented data at the European Hematology Association Congress from two patients with TDT and one patient with severe SCD. AdditionalTo date, more than 30 patients have been ~~enrolled and~~ dosed in ~~both TDT~~the clinical trials to evaluate CTX001 as a potential one-time curative therapy for people with severe SCD and ~~SCD Phase 1/2~~TDT. Enrollment and dosing are ongoing in these clinical ~~trials. In the fourth quarter of 2020,~~trials, and we expect to ~~report clinical data from additional patients treated with CTX001 and data from patients with longer follow-up.~~complete enrollment in 2021.

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•~~The~~In April, the EMA granted Priority Medicines ~~designation~~Designation to CTX001 for the treatment of severe SCD. CTX001 has been granted Regenerative Medicine Advanced Therapy, Fast Track, Orphan Drug and Rare Pediatric Disease designations from the FDA and Orphan Drug Designation from the European Commission for both TDT and SCD.TDT.

Alpha-1 Antitrypsin Deficiency

•We are ~~focused on identifying and developing~~evaluating multiple ~~drug candidates~~compounds with the potential to correct the misfolding of Z-AAT protein in the liver, in order to increase the systemic levels of functional ~~AAT in the blood.~~AAT. Misfolded Z-AAT protein is the root cause of AAT ~~deficiency.~~deficiency and our small molecule corrector program targets both the liver and lung manifestations of the disease.

•~~Enrollment is ongoing~~Patients enrolled in athe Phase 2 proof-of-concept clinical trial for the Z-AAT corrector, ~~VX-864.~~VX-864, have completed the 28-day dosing period. This clinical trial includes a 28-day safety follow-up period that is ongoing. We expect ~~data~~results from this clinical trial in the ~~first half~~second quarter of 2021.

•~~In October 2020, we discontinued development of VX-814 based on the safety and pharmacokinetic profile of VX-814 observed in a Phase 2 clinical trial.~~

APOL1-Mediated Kidney Diseases

•We are evaluating the potential of inhibitors of APOL1 function ~~to reduce proteinuria~~ in people with ~~serious~~APOL1-mediated kidney ~~disease,~~diseases, including focal segmental glomerulosclerosis, or FSGS.

•Enrollment is ongoing in a Phase 2 proof-of-concept clinical trial designed to evaluate the reduction ofin proteinuria in people with APOL1-mediated FSGS after treatment with VX-147. We expect ~~data~~results from this clinical trial in the second half 2021.

Type 1 Diabetes

•We are ~~developing~~evaluating a cell therapy designed to replace insulin-producing islet cells in ~~patients~~people with T1D. We are pursuing two programs for the transplant of these fully-differentiated functional islets into patients: transplantation of islet cells alone, using immunosuppression to protect the implanted cells, and implantation of the islet cells inside a novel immunoprotective device.

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•In March, the U.S. Food and Drug Administration, or FDA, granted Fast Track Designation and we initiated a Phase 1/2 clinical trial evaluating VX-880, our islet cells alone program. This clinical trial involves an infusion of fully differentiated, functional islet cells, and chronic administration of concomitant immunosuppressive therapy, to protect the islet cells from immune rejection.

Pain

•We ~~have completed~~are evaluating selective small molecule inhibitors of NaV1.8, a genetically validated, novel target for the ~~required enabling nonclinical studies and manufacturing work to support~~treatment of pain, with the ~~submission~~goal of ~~an Investigational New Drug, or IND, application~~preventing pain signals traveling from the sensory nerves to the ~~FDA~~central nervous system. We have previously demonstrated clinical proof-of-concept with a small molecule investigational treatment targeting NaV1.8, VX-150, in multiple pain indications including acute pain, neuropathic pain and musculoskeletal pain.

•Our selective NaV1.8 inhibitor, VX-548, demonstrated favorable safety, tolerability and pharmacokinetic profiles in Phase 1 clinical trials. In these clinical trials, the molecule exhibited a favorable profile at doses considerably lower than those required with our previous NaV1.8 inhibitors.

•We expect to advance VX-548 into Phase 2 proof-of-concept clinical trials for acute pain in the second half of 2021.

Investments in External Innovation

•In April, we amended our collaboration with CRISPR for the ~~first program (transplantation~~CTX001 programs in TDT and SCD. Under the terms of ~~islet cells alone) in~~ the ~~fourth quarter~~revised collaboration agreement, we will lead worldwide development, manufacturing and commercialization of ~~2020.~~CTX001. Under the revised collaboration agreement, 60% of the net profits and net losses for CTX001 will be allocated to us and 40% of the net profits and net losses for CTX001 will be allocated to CRISPR. In connection with the closing of the transaction, we will pay a $900.0 million upfront payment to CRISPR and an additional one-time $200.0 million milestone payment upon regulatory approval of CTX001.

•In April, we entered into a research collaboration with Obsidian Therapeutics, Inc., or Obsidian, aimed at the discovery of novel therapies that regulate gene-editing for the treatment of serious diseases. This collaboration enables us to leverage Obsidian’s cytoDRiVE® platform technology to discover gene-editing medicines whose therapeutic activity can be precisely controlled using small molecules.

COVID-19

We continue to monitor the impacts of the COVID-19 global pandemic on our business. COVID-19 has not affected our supply chain or the demand for our medicines, and we believe that we will be able to continue to supply all of our approved medicines to patients globally. We have adjusted our business operations in response to COVID-19, with a majority of our employees continuing to work remotely. We continue to monitor local COVID-19 trends and government guidance for each of our site locations, and ~~we have begun to re-open certain of our sites~~are utilizing a phased, site-specific ~~approach.~~approach to assess employee access to our sites. Currently, all of our research and manufacturing sites are open to essential employees, as permitted by local laws. To provide a safe working environment for our on-site employees, we have, among other things, limited employee numbers at our open sites and increased safety measures, including at home and on-site testing in the U.S., enhanced cleaning and sanitation protocols, required use of personal protective equipment for all on-site employees, hand sanitation stations throughout our open sites and implementation of various social distancing measures while on-site.

Research

We continue to invest in our research programs and foster scientific innovation in order to identify and develop transformative medicines. Our strategy is to combine transformative advances in the understanding of human disease and the science of therapeutics in order to identify and develop new medicines. We believe that pursuing research in diverse areas allows us to balance the risks inherent in drug development and may provide drug candidates that will form our pipeline in future years. To supplement our internal research programs, we acquire technologies and programs and collaborate with biopharmaceutical and technology companies, leading academic research institutions, government laboratories, foundations and other organizations, as needed, to advance research in our areas of therapeutic interest and to access technologies needed to execute on our strategy.

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Drug Discovery and Development

Discovery and development of a new pharmaceutical product is a difficult and lengthy process that requires significant financial resources along with extensive technical and regulatory expertise. Potential drug candidates are subjected to rigorous evaluations, driven in part by stringent regulatory considerations, designed to generate information concerning efficacy, side effects, proper dosage levels and a variety of other physical and chemical characteristics that are important in determining whether a drug candidate should be approved for marketing as a pharmaceutical product. Most chemical compounds that are investigated as potential drug candidates never progress into development, and most drug candidates that do advance into development never receive marketing approval. ~~Because our~~Our investments in drug candidates are subject to considerable ~~risks, we~~risks. We closely monitor the results of our discovery, research, clinical trials and nonclinical studies and frequently evaluate our drug development programs in light of new data and scientific, business and commercial insights, with the objective of balancing risk and potential. This process can result in ~~abrupt~~rapid changes in focus and priorities as new information becomes available and as we gain additional understanding of our ongoing programs and potential new programs, as well as those of our competitors. For example, in ~~October~~ 2020, we discontinued development of VX-814, a drug candidate for the treatment of AAT deficiency, based on the safety and pharmacokinetic profile of VX-814 observed in a Phase 2 clinical trial.

If we believe that data from a completed registration program support approval of a drug candidate, we submit an NDA or BLA to the FDA requesting approval to market the drug candidate in the ~~United States~~U.S. and seek analogous approvals from comparable regulatory authorities in jurisdictions outside the ~~United States.~~U.S. To obtain approval, we must, among other things, demonstrate with evidence gathered in nonclinical studies and well-controlled clinical trials that the drug candidate is safe and effective for the disease it is intended to treat and that the manufacturing facilities, processes and controls for the manufacture of the drug candidate are adequate. The FDA and ex-U.S. regulatory authorities have substantial discretion in deciding whether or not a drug candidate should be granted approval based on the benefits and risks of the drug candidate in the treatment of a particular disease, and could delay, limit or deny regulatory approval. If regulatory delays are significant or regulatory approval is limited or denied altogether, our financial results and the commercial prospects for the drug candidate involved will be harmed.

Regulatory Compliance

Our marketing of pharmaceutical products is subject to extensive and complex laws and regulations. We have a corporate compliance program designed to actively identify, prevent and mitigate risk through the implementation of compliance policies and systems and through the promotion of a culture of compliance. Among other laws, regulations and standards, we are subject to various U.S. federal and state laws, and comparable laws in other jurisdictions, pertaining to health care fraud and abuse, including anti-kickback and false claims laws, and laws prohibiting the promotion of drugs for unapproved or off-label uses. Anti-kickback laws generally make it illegal for a prescription drug manufacturer to knowingly and willfully solicit, offer, receive or pay any remuneration in return for or to induce the referral of business, including the purchase or prescription of a particular drug that is reimbursed by a state or federal health care program. False claims laws prohibit anyone from knowingly or willfully presenting for payment to third-party payors, including Medicare and Medicaid, claims for reimbursed drugs or services that are false or fraudulent, claims for items or services not provided as claimed, or claims for medically unnecessary items or services. We are subject to laws and regulations that regulate the sales and marketing practices of pharmaceutical manufacturers, as well as laws such as the U.S. Foreign Corrupt Practices Act, which govern our international business practices with respect to payments to government officials. In addition, we are subject to various data protection and privacy laws and regulations in the U.S., E.U., U.K., Canada, Australia and other jurisdictions. We expect to continue to devote substantial resources to maintain, administer and expand these compliance programs globally.

Reimbursement

Sales of our products depend, to a large degree, on the extent to which our products are reimbursed by third-party payors, such as government health programs, commercial insurance and managed health care organizations. We dedicate substantial management and other resources in order to obtain and maintain appropriate levels of reimbursement for our products from third-party payors, including governmental organizations in the U.S. and ex-U.S. markets.

In the U.S., we have worked successfully with third party payors in order to promptly obtain appropriate levels of reimbursement for our CF medicines. We plan to continue to engage in discussions with numerous commercial insurers and managed health care organizations, along with government health programs that are typically managed by authorities in the

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individual states, to ensure that payors recognize the significant benefits that our medicines provide by treating the underlying cause of CF and continue to provide access to our medicines.

In Europe and other ex-U.S. markets, we seek government reimbursement for our medicines on a country-by-country basis. This is necessary for each new medicine, as well as for label expansions for our current ~~medicines in most countries.~~medicines. We successfully obtained reimbursement for KALYDECO in each significant ex-U.S. market within two years of approval, but experienced significant challenges in obtaining reimbursement for ORKAMBI in certain ex-U.S. markets. With the completion of reimbursement discussions in England and France in 2019, we have reimbursement for ORKAMBI or SYMKEVI in most of our significant ex-U.S. markets. In addition, in several ex-U.S. markets, including England, Ireland, Denmark and Australia, our reimbursement agreements include innovative arrangements that provide a pathway to access and rapid reimbursement for certain future CF medicines. For example, our existing reimbursement agreements in England, Ireland, and Denmark have been expanded to include KAFTRIO. We expect to continue to focus significant resources to obtain appropriate reimbursement for our products in ex-U.S. markets.

Strategic Transactions

Acquisitions

As part of our business strategy, we seek to acquire drugs, drug candidates and other technologies and businesses that have the potential to complement our ongoing research and development efforts. In 2019, we invested significantly in business development transactions designed to augment our pipeline, including the acquisition of Semma Therapeutics, Inc., or Semma, a privately-held company focused on the use of stem cell-derived human islets as a potentially curative treatment for T1D, and Exonics Therapeutics, Inc., or Exonics, a privately-held company focused on creating transformative gene-editing therapies to repair mutations that cause DMD and other severe neuromuscular diseases, including DM1. In the Semma acquisition, we paid approximately $950.0 million in cash to Semma equity holders. In the Exonics acquisition, we paid approximately $245.0 million upfront to Exonics equity holders and agreed to additional payments based upon successful achievement of specified development and regulatory milestones. We expect to continue to identify and evaluate potential acquisitions ~~that~~and may ~~be similar to~~include larger transactions or ~~different from the transactions that we have engaged in previously.~~

Both of our 2019 acquisitions were accounted for as business combinations. As of the acquisition date for each transaction, the cash payments, as well as the fair value of contingent consideration for Exonics, were allocated primarily to goodwill and the fair value of several in-process research and development assets that we acquired. The fair value of contingent consideration related to Exonics was recorded as a liability and will be adjusted on a quarterly basis in the future. As a result, these acquisitions are primarily reflected in additional assets and liabilities on our condensed consolidated balance sheet. Please refer to Note C, “Acquisitions,” and our critical accounting policies, “Acquisitions,” in our 2019 Annual Report on Form 10-K for further information regarding the significant judgments and estimates related to our 2019 acquisitions.later-stage assets.

Collaboration and Licensing Arrangements

We enter into arrangements with third parties, including collaboration and licensing arrangements, for the development, manufacture and commercialization of drugs, drug candidates and other technologies that have the potential to complement our ongoing research and development efforts. We expect to continue to identify and evaluate collaboration and licensing opportunities that may be similar to or different from the collaborations and licenses that we have engaged in previously.

In-License Agreements

We have entered into collaborations with biotechnology and pharmaceutical companies in order to acquire rights or to license drug candidates or technologies that enhance our pipeline and/or our research capabilities. Over the last several years, we entered into collaboration agreements with a number of companies, including Affinia Therapeutics, Inc., Arbor Biotechnologies, Inc., CRISPR, Kymera Therapeutics, Inc., Moderna, ~~and~~Inc., Molecular Templates, Inc., Obsidian, and Skyhawk Therapeutics, Inc. Generally, when we in-license a technology or drug candidate, we make upfront payments to the collaborator, assume the costs of the program and/or agree to make contingent payments, which could consist of milestone, royalty and option payments. Most of these collaboration payments are expensed as research and development expenses; however, depending on many factors, including the structure of the collaboration, the significance of the in-licensed drug candidate to the collaborator’s operations and the other activities in which our collaborators are engaged, the accounting for these transactions can vary significantly. In the

~~Table~~ first quarter of ~~Contents~~

~~nine months ended September 30,~~2021 and 2020, ~~and 2019,~~ our research and development expenses included ~~$143.3~~$1.7 million and ~~$261.6~~$36.3 million, respectively, related to upfront and milestones payments pursuant to our collaboration agreements.

Joint Development and Commercialization Agreement with CRISPR

In 2017, we entered into a joint development and commercialization agreement, or JDCA, with CRISPR pursuant to which we are co-developing and preparing to co-commercialize CTX001 for TDT and SCD. This JDCA was entered into following our exercise of an option to co-develop and co-commercialize the hemoglobinopathies program that was contained in the collaboration agreement that we entered into with CRISPR in 2015.

In April 2021, we and CRISPR entered into an amended and restated joint development and commercialization agreement, or A&R JDCA. Under the terms of the A&R JDCA, we will lead worldwide development, manufacturing and commercialization of CTX001. Additionally, 60% of the net profits and net losses for CTX001 will be allocated to us and

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40% of the net profits and net losses for CTX001 will be allocated to CRISPR. In connection with the closing of the transaction, we will pay a $900.0 million upfront payment to CRISPR and an additional one-time $200.0 million milestone payment upon regulatory approval of CTX001. The closing of the transaction contemplated by the A&R JDCA is subject to certain conditions including the expiration of the waiting period under the Hart-Scott-Rodino Antitrust Improvements Act and any other required antitrust clearance. We expect to record the $900.0 million upfront payment to “Research and development expenses” upon closing of the transaction contemplated by the A&R JDCA.

Out-License Agreements

We also have out-licensed internally developed programs to collaborators who are leading the development of these programs. These out-license arrangements include our agreement with Merck KGaA, Darmstadt, Germany, which licensed oncology research and development programs from us in early 2017. Pursuant to these out-licensing arrangements, our collaborators are responsible for the research, development and commercialization costs associated with these programs, and we are entitled to receive contingent milestone and/or royalty payments. As a result, we do not expect to incur significant expenses in connection with these programs and have the potential for future collaborative and royalty revenues resulting from these programs.

Please refer to Note C, “Collaborative Arrangements,” for further information regarding our in-license agreements and out-license agreements.

Strategic Investments

In connection with our business development activities, we have periodically made equity investments in our collaborators. As of ~~September 30, 2020,~~March 31, 2021, we held strategic equity investments in public companies and certain private companies, and we plan to make additional strategic equity investments in the future. While we invest the majority of our cash, cash equivalents and marketable securities in instruments that meet specific credit quality standards and limit our exposure to any one issue or type of instrument, our strategic investments are maintained and managed separately from our other cash, cash equivalents and marketable securities. Any changes in the fair value of equity investments with readily determinable fair values (including publicly traded securities) are recorded to other income (expense), net in our condensed consolidated statement of operations. For equity investments without readily determinable fair values including equity investments in private companies, each reporting period we are required to re-evaluate the carrying value of the investment, which may result in other income (expense).

In the ~~nine months ended September 30,~~first quarter of 2021 and 2020, ~~and 2019,~~ we recorded within other income (expense), ~~net gains~~losses of ~~$140.9~~$52.3 million and ~~$68.9~~$44.9 million, respectively, related to changes in the fair value of our strategic investments, and from sales of certain equity investments. As of March 31, 2021, the fair value of our investments in publicly traded companies was $143.5 million. To the extent that we continue to hold strategic investments, particularly strategic investments in publicly traded companies, we will record other income (expense) related to these strategic investments on a quarterly basis. Due to the increased volatility of the global markets, including as a result of COVID-19, and the high volatility of stocks in the biotechnology industry, we expect the value of these strategic investments to fluctuate and that the increases or decreases in the fair value of these strategic investments will continue to have material impacts on our net income (expense) and our profitability on a quarterly and/or annual basis.

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RESULTS OF OPERATIONS


		Three Months Ended September 30,				Increase/(Decrease)				Nine Months Ended September 30,				Increase/(Decrease)					Three Months Ended March 31,			Increase/(Decrease)
		2020		2019		$		%		2020		2019		$		%						2021		2020		$		%
		(in thousands, except percentages and per share amounts)																				(in thousands, except percentages and per share amounts)
Revenues	Revenues	$	1,538,271	$	949,828	$	588,443	62	%	$	4,577,863	$	2,749,556	$	1,828,307	66	%	Revenues				$	1,724,305	$	1,515,107	$	209,198	14	%
Operating costs and expenses	Operating costs and expenses	866,030		850,495		15,535		2	%	2,467,365		2,103,455		363,910		17	%	Operating costs and expenses				836,479		794,883		41,596		5	%
Income from operations	Income from operations	672,241		99,333		572,908		577	%	2,110,498		646,101		1,464,397		227	%	Income from operations				887,826		720,224		167,602		23	%
Other non-operating income (expense), net		73,630		(28,667)		102,297		**		117,677		71,868		45,809		64	%
Other non-operating expense, net																		Other non-operating expense, net				(66,866)		(62,690)		(4,176)		7	%
Provision for income taxes	Provision for income taxes	78,437		13,148		65,289		497	%	120,718		124,393		(3,675)		(3)	%	Provision for income taxes				167,822		54,781		113,041		206	%
Net income	Net income	$	667,434	$	57,518	$	609,916	1,060	%	$	2,107,457	$	593,576	$	1,513,881	255	%	Net income				$	653,138	$	602,753	$	50,385	8	%

Net income per diluted common share	Net income per diluted common share	$	2.53	$	0.22					$	7.98	$	2.28					Net income per diluted common share		$	2.49	$	2.29
Diluted shares used in per share calculations	Diluted shares used in per share calculations	264,079		260,473						264,031		260,182						Diluted shares used in per share calculations				261,916		263,515

														** Not meaningful

Net Income

Our net income increased in the ~~third~~first quarter of ~~2020~~2021 as compared to the ~~third~~first quarter of ~~2019~~2020 primarily due to increased revenues resulting from the ~~U.S. approval~~uptake of KAFTRIO in Europe and continued performance of TRIKAFTA in the ~~fourth quarter of 2019 and continued uptake of our medicines in ex-U.S. markets.~~U.S. Our ~~net income in the third quarter of 2020 as compared to the third quarter of 2019 also~~ increased ~~due to an increase in the fair value of our strategic investments and decreased collaborative research and development payments,~~revenues were partially offset by increased operating costs and expenses, primarily as a result of increased cost of sales consistent with increased product revenues, ~~increased sales, general and administrative expenses to support our business~~ and an ~~increased~~increase in the provision for income taxes. The increase in our provision for income taxes ~~due to~~was the result of our ~~increasing profitability.~~

~~Our net income~~ increased profitability and a discrete tax benefit recognized in the ~~nine months ended September 30,~~first quarter of 2020 as compared to the nine months ended September 30, 2019 primarily due to increased revenues partially offset by increased operating costs and expenses. The increased revenues were primarily due to the U.S. approval of TRIKAFTAfor which there was no corresponding benefit in the ~~fourth~~first quarter of 2019 and continued uptake of our medicines in ex-U.S. markets. The increased operating expenses were primarily due to increased cost of sales consistent with increased product revenues, increased investment in research and development and increased sales, general and administrative expenses to support our business.

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2021.

Revenues


		Three Months Ended September 30,				Increase/(Decrease)				Nine Months Ended September 30,				Increase/(Decrease)					Three Months Ended March 31,	Increase/(Decrease)
		2020		2019		$		%		2020		2019		$		%				2021		2020		$		%
		(in thousands, except percentages)																		(in thousands, except percentages)
Product revenues, net	Product revenues, net	$	1,536,271	$	949,828	$	586,443	62	%	$	4,575,863	$	2,747,461	$	1,828,402	67	%	Product revenues, net		$	1,723,305	$	1,515,107	$	208,198	14	%
Collaborative and royalty revenues		2,000		—		2,000		**		2,000		2,095		(95)		(5)	%
Other revenues																		Other revenues		1,000		—		1,000		**
Total revenues	Total revenues	$	1,538,271	$	949,828	$	588,443	62	%	$	4,577,863	$	2,749,556	$	1,828,307	66	%	Total revenues		$	1,724,305	$	1,515,107	$	209,198	14	%

														** Not meaningful										** Not meaningful

Product Revenues, Net


		Three Months Ended September 30,				Increase/(Decrease)				Nine Months Ended September 30,				Increase/(Decrease)					Three Months Ended March 31,	Increase/(Decrease)
		2020		2019		$		%		2020		2019		$		%				2021		2020		$		%
		(in thousands, except percentages)																		(in thousands, except percentages)
TRIKAFTA/KAFTRIO	TRIKAFTA/KAFTRIO	$	960,308	$	—	$	960,308	**		$	2,773,256	$	—	$	2,773,256	**		TRIKAFTA/KAFTRIO		$	1,193,217	$	895,233	$	297,984	33	%
SYMDEKO/SYMKEVI	SYMDEKO/SYMKEVI	156,178		403,714		(247,536)		(61)	%	501,066		1,085,821		(584,755)		(54)	%	SYMDEKO/SYMKEVI		125,049		173,159		(48,110)		(28)	%
ORKAMBI	ORKAMBI	225,919		296,711		(70,792)		(24)	%	692,038		906,159		(214,121)		(24)	%	ORKAMBI		218,697		234,138		(15,441)		(7)	%
KALYDECO	KALYDECO	193,866		249,403		(55,537)		(22)	%	609,503		755,481		(145,978)		(19)	%	KALYDECO		186,342		212,577		(26,235)		(12)	%
Total product revenues, net	Total product revenues, net	$	1,536,271	$	949,828	$	586,443	62	%	$	4,575,863	$	2,747,461	$	1,828,402	67	%	Total product revenues, net		$	1,723,305	$	1,515,107	$	208,198	14	%

														** Not meaningful

In the ~~third~~first quarter ~~and nine months ended September 30, 2020,~~of 2021, our net product revenues increased by ~~$586.4~~$208.2 million ~~and $1.83 billion, respectively,~~ as compared to the ~~third~~first quarter ~~and nine months ended September 30, 2019.~~of 2020. The increase in ~~total~~our net product revenues in the first quarter of 2021 was primarily due to the uptake of KAFTRIO, which was approved in Europe in the third quarter of 2020, and ~~nine months ended September 30, 2020 was primarily due to~~ the ~~launch~~continued performance of TRIKAFTA ~~which was approved~~ in the ~~United States in the fourth quarter of 2019.~~U.S. Decreases in revenues for our products other ~~products~~than TRIKAFTA/KAFTRIO were primarily the result of patients ~~in the United States~~ switching from these medicines to ~~TRIKAFTA, partially offset by label expansions and expanded access to our medicines in ex-U.S markets.~~TRIKAFTA/KAFTRIO. In the ~~third~~first quarter of 2021 and ~~nine months ended September 30,~~ 2020, our net product revenues included ~~$313.7~~$469.9 million and ~~$955.4~~$327.5 million, respectively, from ex-U.S. markets. In

Other Revenues

Our other revenues were $1.0 million related to a collaborative milestone that we earned in the ~~third quarter and nine months ended September 30, 2019, our net product revenues included $239.5 million and $697.6 million, respectively, from ex-U.S. markets. In the third~~first quarter of ~~2020, KAFTRIO was approved in the E.U., which we anticipate will positively affect our net product revenues in the future.~~

~~Collaborative and Royalty Revenues~~

~~Our collaborative and royalty revenues were $2.0 million in the third quarter and nine months ended September 30, 2020, respectively.~~2021. We did not record any ~~collaborative and royalty~~other revenues in the ~~third~~first quarter of ~~2019. In the nine months ended September 30, 2019, our collaborative and royalty revenues were $2.1 million.~~2020. Our ~~collaborative~~other revenues have historically fluctuated significantly from one period to another based on our collaborative out-license activities, and may continue to fluctuate in the future. Our

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future royalty revenues will be dependent on if, and when, our collaborators ~~including Merck KGaA, Darmstadt, Germany,~~ are able to successfully develop drug candidates that we have out-licensed to them.

Operating Costs and Expenses

` Three Months Ended September 30, Increase/(Decrease) Nine Months Ended September 30, Increase/(Decrease)
2020 2019 $ % 2020 2019 $ %
(in thousands, except percentages)
Cost of sales $ 186,182 $ 131,914 $ 54,268 41 % $ 533,199 $ 362,746 $ 170,453 47 %
Research and development expenses 493,497 555,948 (62,451) (11) % 1,362,953 1,274,529 88,424 7 %
Sales, general and administrative expenses 184,551 159,674 24,877 16 % 558,613 463,221 95,392 21 %
Change in fair value of contingent consideration 1,800 2,959 (1,159) (39) % 12,600 2,959 9,641 326 %
Total costs and expenses $ 866,030 $ 850,495 $ 15,535 2 % $ 2,467,365 $ 2,103,455 $ 363,910 17 %

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`	Three Months Ended March 31,	Increase/(Decrease)
		2021		2020		$		%
		(in thousands, except percentages)
Cost of sales		$	192,329	$	162,497	$	29,832	18	%
Research and development expenses		455,973		448,528		7,445		2	%
Sales, general and administrative expenses		192,077		182,258		9,819		5	%
Change in fair value of contingent consideration		(3,900)		1,600		(5,500)		**
Total costs and expenses		$	836,479	$	794,883	$	41,596	5	%

				** Not meaningful

Cost of Sales

Our cost of sales primarily consists of third-party royalties payable on our net sales of our products as well as the cost of producing inventories that corresponded to product revenues for the reporting ~~period, plus the third-party royalties payable on our net sales of our products.~~period. Pursuant to our agreement with the Cystic Fibrosis Foundation, or CFF, our tiered third-party royalties on sales of TRIKAFTA/KAFTRIO, SYMDEKO/SYMKEVI, KALYDECO and ORKAMBI, calculated as a percentage of net sales, range from the single digits to the sub-teens, with royalties on sales of TRIKAFTA/KAFTRIO slightly lower than for our other products. Over the last several years, our cost of sales has been increasing due to increased net product revenues. Our cost of sales as a percentage of our net product revenues was approximately ~~12% and 14%~~11% in each of the ~~third~~first quarter of ~~2020~~2021 and ~~2019, respectively. Our cost of sales as a percentage of our net product revenues was approximately 12% and 13% in the nine months ended September 30,~~ 2020, ~~and 2019,~~ respectively.

Research and Development Expenses


		Three Months Ended September 30,				Increase/(Decrease)				Nine Months Ended September 30,				Increase/(Decrease)					Three Months Ended March 31,	Increase/(Decrease)
		2020		2019		$		%		2020		2019		$		%				2021		2020		$		%
		(in thousands, except percentages)																		(in thousands, except percentages)
Research expenses	Research expenses	$	186,152	$	302,418	$	(116,266)	(38)	%	$	477,560	$	537,509	$	(59,949)	(11)	%	Research expenses		$	129,748	$	157,270	$	(27,522)	(17)	%
Development expenses	Development expenses	307,345		253,530		53,815		21	%	885,393		737,020		148,373		20	%	Development expenses		326,225		291,258		34,967		12	%
Total research and development expenses	Total research and development expenses	$	493,497	$	555,948	$	(62,451)	(11)	%	$	1,362,953	$	1,274,529	$	88,424	7	%	Total research and development expenses		$	455,973	$	448,528	$	7,445	2	%

Our research and development expenses include internal and external costs incurred for research and development of our drugs and drug candidates and expenses related to certain technology that we acquire or license through business development transactions. We do not assign our internal costs, such as salary and benefits, stock-based compensation expense, laboratory supplies and other direct expenses and infrastructure costs, to individual drugs or drug candidates, because the employees within our research and development groups typically are deployed across multiple research and development programs. These internal costs are significantly greater than our external costs, such as the costs of services provided to us by clinical research organizations and other outsourced research, which we allocate by individual program. All research and development costs for our drugs and drug candidates are expensed as incurred.

Since January ~~2018,~~2019, we have incurred approximately ~~$4.5~~$4.0 billion in research and development expenses associated with drug discovery and development. The successful development of our drug candidates is highly uncertain and subject to a number of risks. In addition, the duration of clinical trials may vary substantially according to the type, complexity and novelty of the drug candidate and the disease indication being targeted. The FDA and comparable agencies in foreign countries impose substantial requirements on the introduction of therapeutic pharmaceutical products, typically requiring lengthy and detailed laboratory and clinical testing procedures, sampling activities and other costly and time-consuming procedures. Data obtained from nonclinical and clinical activities at any step in the testing process may be adverse and lead to discontinuation or redirection of development activities. Data obtained from these activities also are susceptible to varying interpretations, which could delay, limit or prevent regulatory approval. The duration and cost of discovery, nonclinical studies and clinical trials may vary significantly over the life of a project and are difficult to predict. Therefore, accurate and meaningful estimates of the ultimate costs to bring our drug candidates to market are not available.

In ~~2019~~2020 and the ~~nine months ended September 30, 2020,~~first quarter of 2021, costs related to our CF programs represented the largest portion of our development costs. Any estimates regarding development and regulatory timelines for our drug candidates are highly subjective and

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subject to change. Until we have data from Phase 3 clinical trials, we cannot make a meaningful estimate regarding when, or if, a clinical development program will generate revenues and cash flows.

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Research Expenses


		Three Months Ended September 30,				Increase/(Decrease)				Nine Months Ended September 30,				Increase/(Decrease)					Three Months Ended March 31,	Increase/(Decrease)
		2020		2019		$		%		2020		2019		$		%				2021		2020		$		%
		(in thousands, except percentages)																		(in thousands, except percentages)
Research Expenses:	Research Expenses:																	Research Expenses:
Salary and benefits	Salary and benefits	$	32,145	$	33,767	$	(1,622)	(5)	%	$	97,513	$	80,644	$	16,869	21	%	Salary and benefits		$	34,742	$	34,269	$	473	1	%
Stock-based compensation expense	Stock-based compensation expense	15,301		16,170		(869)		(5)	%	68,206		50,843		17,363		34	%	Stock-based compensation expense		21,002		26,409		(5,407)		(20)	%
Outsourced services and other direct expenses	Outsourced services and other direct expenses	27,911		27,721		190		1	%	79,837		78,707		1,130		1	%	Outsourced services and other direct expenses		40,106		30,853		9,253		30	%
Collaborative payments	Collaborative payments	80,050		198,979		(118,929)		(60)	%	143,300		251,179		(107,879)		(43)	%	Collaborative payments		1,650		36,250		(34,600)		(95)	%
Infrastructure costs	Infrastructure costs	30,745		25,781		4,964		19	%	88,704		76,136		12,568		17	%	Infrastructure costs		32,248		29,489		2,759		9	%
Total research expenses	Total research expenses	$	186,152	$	302,418	$	(116,266)	(38)	%	$	477,560	$	537,509	$	(59,949)	(11)	%	Total research expenses		$	129,748	$	157,270	$	(27,522)	(17)	%

We expect to continue to invest in our research programs with a focus on ~~identifying drug candidates with the goal of~~ creating transformative medicines for serious diseases. Our research expenses ~~decreased by 38%~~have historically fluctuated, and are expected to continue to fluctuate, from one period to another due to upfront and milestone payments related to our business development activities that are reflected in the ~~third quarter of 2020~~preceding table as ~~compared to the third quarter of 2019 primarily due to a decrease in~~ collaborative payments. Our research expenses, ~~decreased by 11% in the nine months ended September 30, 2020 as compared to the nine months ended September 30, 2019, primarily due to a decrease in~~excluding these collaborative payments, ~~partially offset by increased expenses to support~~have been increasing over the last several years as we have invested in our pipeline and expanded our cell and genetic therapy ~~programs.~~capabilities.

Development Expenses


		Three Months Ended September 30,				Increase/(Decrease)				Nine Months Ended September 30,				Increase/(Decrease)					Three Months Ended March 31,	Increase/(Decrease)
		2020		2019		$		%		2020		2019		$		%				2021		2020		$		%
		(in thousands, except percentages)																		(in thousands, except percentages)
Development Expenses:	Development Expenses:																	Development Expenses:
Salary and benefits	Salary and benefits	$	73,698	$	59,552	$	14,146	24	%	$	221,828	$	178,254	$	43,574	24	%	Salary and benefits		$	84,530	$	79,598	$	4,932	6	%
Stock-based compensation expense	Stock-based compensation expense	45,469		36,334		9,135		25	%	135,526		117,008		18,518		16	%	Stock-based compensation expense		51,800		46,278		5,522		12	%
Outsourced services and other direct expenses	Outsourced services and other direct expenses	133,595		107,439		26,156		24	%	374,926		298,908		76,018		25	%	Outsourced services and other direct expenses		132,812		116,433		16,379		14	%
Collaborative payments		—		5,000		(5,000)		**		—		10,440		(10,440)		**
Infrastructure costs	Infrastructure costs	54,583		45,205		9,378		21	%	153,113		132,410		20,703		16	%	Infrastructure costs		57,083		48,949		8,134		17	%
Total development expenses	Total development expenses	$	307,345	$	253,530	$	53,815	21	%	$	885,393	$	737,020	$	148,373	20	%	Total development expenses		$	326,225	$	291,258	$	34,967	12	%

														** Not meaningful

Our development expenses increased by ~~21%~~12% in the ~~third~~first quarter of ~~2020~~2021 as compared to the ~~third~~first quarter of ~~2019 and increased by 20% in the nine months ended September 30,~~ 2020, ~~as compared to the nine months ended September 30, 2019,~~ primarily due to increased expenses related to our ~~diverse~~diversifying pipeline, including clinical trials, headcount and infrastructure costs. Upon closing of the transaction contemplated by the A&R JDCA, we expect to record our $900.0 million upfront payment to CRISPR as a development expense.

Sales, General and Administrative Expenses

Three Months Ended September 30, Increase/(Decrease) Nine Months Ended September 30, Increase/(Decrease)
2020 2019 $ % 2020 2019 $ %
(in thousands, except percentages)
Sales, general and administrative expenses $ 184,551 $ 159,674 $ 24,877 16 % $ 558,613 $ 463,221 $ 95,392 21 %


	Three Months Ended March 31,	Increase/(Decrease)
		2021		2020		$		%
		(in thousands, except percentages)
Sales, general and administrative expenses		$	192,077	$	182,258	$	9,819	5	%

Sales, general and administrative expenses increased by ~~16%~~5% in the ~~third~~first quarter of ~~2020~~2021 as compared to the ~~third~~first quarter of ~~2019 and increased by 21% in the nine months ended September 30,~~ 2020, ~~as compared to the nine months ended September 30, 2019,~~ primarily due to ~~increased global support for our medicines, including~~the incremental investment to support the ~~launch~~commercialization of our ~~triple combination regimen~~medicines and increased support for our CF pipeline products and other disease areas.

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Contingent Consideration

~~In the third quarter and nine months ended September 30, 2020, the increase in the~~The fair value of contingent consideration potentially payable to Exonics’ former equity holders ~~was $1.8~~decreased $3.9 million ~~and $12.6 million, respectively. In each of the third quarter and nine months ended September 30, 2019, the increase~~ in the ~~fair value~~first quarter of ~~contingent consideration potentially payable to Exonics’ former equity holders was $3.0 million.~~2021 and increased $1.6 million in the first quarter of 2020.

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Other Non-Operating Income (Expense), Net

Interest Income

Interest income decreased from ~~$17.6 million and $51.3~~$12.6 million in the ~~third~~first quarter ~~and nine months ended September 30, 2019, respectively,~~of 2020 to ~~$3.1 million and $19.9~~$1.5 million in the ~~third~~first quarter ~~and nine months ended September 30, 2020, respectively,~~of 2021 primarily due to a decrease in prevailing market interest ~~rates.~~rates despite an increase in our cash equivalents and available-for-sale debt securities. Our future interest income will be dependent on the amount of, and prevailing market interest rates on, our outstanding cash equivalents and ~~marketable~~available-for-sale debt securities.

Interest Expense

Interest expense was ~~$13.9 million and $41.9~~$15.7 million in the ~~third~~first quarter ~~and nine months ended September 30, 2020, respectively,~~of 2021 as compared to ~~$14.5 million and $44.3~~$14.1 million in the ~~third~~first quarter ~~and nine months ended September 30, 2019, respectively.~~of 2020. The majority of our interest expense in these periods was related to imputed interest expense associated with our leased corporate headquarters in Boston. Our future interest expense will be dependent on whether, and to what extent, we borrow amounts under our credit facilities.

Other Income (Expense), Net

~~Other~~We recorded expenses of $52.7 million and $61.1 million to other income (expense), net ~~was income of $84.4 million and $139.6 million~~ in the ~~third~~first quarter of 2021 and ~~nine months ended September 30,~~ 2020, ~~respectively, as compared to an expense of $31.7 million and income of $64.8 million in the third quarter and nine months ended September 30, 2019,~~ respectively. Our other income (expense), net in these periods was primarily related to changes in the fair value of our strategic ~~investments, as well as realized gains from sales of certain~~ investments. We expect that due to the volatility of the stock price of biotechnology companies, our other income (expense), net will fluctuate in future periods based on increases or decreases in the fair value of our strategic investments.

Income Taxes

Our provision for income taxes was ~~$78.4~~$167.8 million and ~~$120.7~~$54.8 million in the ~~third~~first quarter of 2021 and ~~nine months ended September 30,~~ 2020, ~~respectively, as compared to $13.1 million and $124.4 million in the third quarter and nine months ended September 30, 2019,~~ respectively. Our effective tax rate of 20% for the ~~nine months ended September 30, 2020 was lower than the U.S. statutory rate primarily due to (i) discrete tax benefits associated with the $209.0 million transfer~~first quarter of intellectual property rights to the United Kingdom, the write-off of a long-term intercompany receivable, and an increase in the United Kingdom’s corporate tax rate; and (ii) excess tax benefits related to stock-based compensation. Our effective tax rate for the nine months ended September 30, 20192021 was lower than the U.S. statutory rate primarily due to excess tax benefits related to stock-based compensation. We released our valuation allowance on the majority of our net operating losses and other deferred tax assets in the fourth quarter of 2018. Starting in 2019, we began recording a provision for income taxes on our pre-tax income using anOur effective tax rate ~~approximating~~of 8% for the first quarter of 2020 was lower than the U.S. statutory ~~rates. We expect~~rate primarily due to ~~utilize our remaining previously benefited U.S. net operating losses in 2020. As~~ a ~~result,~~discrete benefit related to the write off of a ~~larger portion of our~~long-term intercompany receivable and excess tax ~~provision will represent a cash tax payable in future periods.~~benefits related to stock-based compensation.

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LIQUIDITY AND CAPITAL RESOURCES

The following table summarizes the components of our financial condition as of ~~September 30, 2020~~March 31, 2021 and December 31, ~~2019:~~2020:


		September 30,		December 31,		Increase/(Decrease)					March 31,		December 31,		Increase/(Decrease)
		2020		2019		$		%			2021		2020		$		%
		(in thousands)									(in thousands)
Cash, cash equivalents and marketable securities	Cash, cash equivalents and marketable securities	$	6,151,058	$	3,808,294	$	2,342,764	62	%	Cash, cash equivalents and marketable securities	$	6,923,968	$	6,658,897	$	265,071	4	%
Working Capital	Working Capital									Working Capital
Total current assets	Total current assets	7,458,456		4,822,829		2,635,627		55	%	Total current assets	8,539,307		8,133,379		405,928		5	%
Total current liabilities	Total current liabilities	(2,004,026)		(1,334,827)		669,199		50	%	Total current liabilities	(1,944,050)		(1,877,533)		66,517		4	%
Total working capital	Total working capital	$	5,454,430	$	3,488,002	$	1,966,428	56	%	Total working capital	$	6,595,257	$	6,255,846	$	339,411	5	%

As of ~~September 30, 2020,~~March 31, 2021, total working capital was ~~$5.5~~$6.6 billion, which represented an increase of ~~$2.0 billion~~$339 million from ~~$3.5~~$6.3 billion as of December 31, ~~2019.~~2020. The increase in total working capital in the ~~nine months ended September 30, 2020~~first quarter of 2021 was primarily related to ~~$2.8 billion~~$921.1 million of cash provided by operations partially offset by ~~$408.0~~$425.0 million of cash used to repurchase our common stock pursuant to ~~the~~our share repurchase program ~~that we announced in July 2019~~ and expenditures for property and equipment of ~~$212.1~~$70.9 million.

Sources of Liquidity

As of ~~September 30, 2020,~~March 31, 2021, we had cash, cash equivalents and marketable securities of ~~$6.2~~$6.9 billion, which represented an increase of ~~$2.3 billion~~$265.1 million from ~~$3.8~~$6.7 billion as of December 31, ~~2019.~~2020. We intend to rely on our existing cash, cash equivalents and marketable securities together with cash flows from product sales as our primary source of liquidity.

We may borrow up to a total of $2.5 billion pursuant to two revolving credit facilities. We may repay and reborrow amounts under these revolving credit agreements without penalty. Subject to certain conditions, we may request that the

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borrowing capacity for each of the credit agreements be increased by an additional $500.0 million, for a total of $3.5 billion collectively.

Other possible sources of future liquidity include commercial debt, public and private offerings of our equity and debt securities, strategic sales of assets or businesses and financial transactions. Negative covenants in our credit agreement may prohibit or limit our ability to access these sources of liquidity. As of March 31, 2021, we were in compliance with these covenants.

Future Capital Requirements

We have significant future capital requirements, including:

•significant expected operating expenses to conduct research and development activities and to operate our organization; and

•substantial facility and ~~capital~~finance lease obligations.

In addition:

•We have entered into certain collaboration agreements with third parties that include the funding of certain research, development and commercialization ~~efforts with~~efforts. Certain of our business development transactions, including collaborations and acquisitions, include the potential for future milestone and royalty payments by us upon the achievement of pre-established developmental and regulatory targets and/or commercial ~~targets, and we~~targets. We may enter into additional business development transactions, including acquisitions, collaborations and equity investments, that require additional capital.

•In 2019, we reached an agreement with the French government and agreed to repay a portion of the amounts we have collected under the ORKAMBI early access programs in France to the French government in the fourth quarter of 2020 based on the difference between the invoiced amount and the final amount for ORKAMBI distributed through these programs as reflected in the structure of the agreement with the French government.

•To the extent we borrow amounts under the credit agreements we entered into in ~~2019~~2020 and ~~2020,~~2019, we would be required to repay any outstanding principal amounts in 2022 or 2024, ~~or 2022,~~ respectively.

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•AsUpon closing of ~~September 30, 2020, $56.0~~the transaction contemplated by the A&R JDCA, we will pay a $900.0 million ~~remained available~~upfront payment to ~~fund repurchases under our share repurchase program.~~CRISPR.

We expect that cash flows from our products together with our current cash, cash equivalents and marketable securities will be sufficient to fund our operations for at least the next twelve months and do not expect COVID-19 to have an adverse effect on our liquidity. The adequacy of our available funds to meet our future operating and capital requirements will depend on many factors, including the amounts of future revenues generated by our products, and the potential introduction of one or more of our other drug candidates to the market, the level of our business development activities and the number, breadth, cost and prospects of our research and development programs.

Financing Strategy

We may raise additional capital by borrowing under credit agreements, through public offerings or private placements of our securities or securing new collaborative agreements or other methods of financing. We will continue to manage our capital structure and will consider all financing opportunities, whenever they may occur, that could strengthen our long-term liquidity profile. There can be no assurance that any such financing opportunities will be available on acceptable terms, if at all.

CONTRACTUAL COMMITMENTS AND OBLIGATIONS

Our commitments and obligations were reported in our Annual Report on Form 10-K for the year ended December 31, ~~2019,~~2020, which was filed with the Securities and Exchange Commission, or SEC, on February ~~13, 2020. There~~11, 2021. Except for the following, there have been no material changes from the contractual commitments and obligations previously disclosed in that Annual Report on Form ~~10-K.~~10-K:

•Upon closing of the transaction contemplated by the A&R JDCA, we will pay a $900.0 million upfront payment to CRISPR, and CRISPR may earn an additional one-time $200.0 million milestone payment upon receipt of the first marketing approval of CTX001 from the FDA or the European Commission.

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CRITICAL ACCOUNTING POLICIES AND ESTIMATES

Our discussion and analysis of our financial condition and results of operations are based upon our condensed consolidated financial statements prepared in accordance with generally accepted accounting principles in the ~~United States.~~U.S. The preparation of these financial statements requires us to make certain estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements and the reported amounts of revenues and expenses during the reported periods. These items are monitored and analyzed by management for changes in facts and circumstances, and material changes in these estimates could occur in the future. Changes in estimates are reflected in reported results for the period in which the change occurs. We base our estimates on historical experience and various other assumptions that we believe to be reasonable under the circumstances. Actual results may differ from our estimates if past experience or other assumptions do not turn out to be substantially accurate. During the ~~nine~~three months ended ~~September 30, 2020,~~March 31, 2021, there were no material changes to our critical accounting policies as reported in our Annual Report on Form 10-K for the year ended December 31, ~~2019,~~2020, which was filed with the SEC on February ~~13, 2020.~~11, 2021.

RECENT ACCOUNTING PRONOUNCEMENTS

For a discussion of recent accounting pronouncements, please refer to Note A, “Basis of Presentation and Accounting Policies.”

Item 3. Quantitative and Qualitative Disclosures About Market Risk

As part of our investment portfolio, we own financial instruments that are sensitive to market risks. The investment portfolio is used to preserve our capital. None of these market risk-sensitive instruments are held for trading purposes. We do not have derivative financial instruments in our investment portfolio.

~~Interest Rate Risk~~

We invest our cash in a variety of financial instruments, principally securities issued by the U.S. government and its agencies, investment-grade corporate bonds and commercial paper, and money market funds. These investments are denominated in U.S. Dollars. All of our interest-bearing securities are subject to interest rate risk and could decline in value if interest rates fluctuate, including potential fluctuations as a result of COVID-19. Substantially all of our investment portfolio consists of marketable securities with active secondary or resale markets to help ensure portfolio liquidity, and we have implemented guidelines limiting the term-to-maturity of our investment instruments. Due to the conservative nature of these instruments, we do not believe that we have a material exposure to interest rate risk. If interest rates were to increase or decrease by 1%, the fair value of our investment portfolio would increase or decrease by an immaterial amount.

We entered into a credit agreement in each of 2019 and 2020. Loans under these credit agreements bear interest, at our option, at either a base rate or a Eurocurrency rate, in each case plus an applicable margin based on our consolidated leverage ratio (the ratio of our total consolidated funded indebtedness to our consolidated EBITDA for the most recently completed four fiscal quarter period). Pursuant to the credit agreement that we entered into in 2019, the applicable margin on base rate loans ranges from 0.125% to 0.500% and the applicable margin on Eurocurrency loans ranges from 1.125% to 1.500%. Pursuant to the credit agreement that we entered into in 2020, the applicable margin on base rate loans ranges from 0.500% to 0.875% and the applicable margin on Eurocurrency loans ranges from 1.500% to 1.875%. We do not believe that changes in interest rates related to either credit agreement would have a material effect on our financial statements. As of September 30, 2020, we had no principal or interest outstanding under either of our existing credit facilities. A portion of our “Interest expense” in the fourth quarter of 2020 will be dependent on whether, and to what extent, we borrow amounts under these existing facilities.

~~Foreign Exchange Market Risk~~

As a result of our foreign operations, we face exposure to movements in foreign currency exchange rates, primarily the Euro and British Pound against the U.S. Dollar. Fluctuations in the global markets, including as a result of COVID-19, may have a positive or negative effect on our foreign exchange rate exposure. The current exposures arise primarily from cash, accounts receivable, intercompany receivables and payables, payables and accruals and inventories. Both positive and negative effects to our net revenues from international product sales from movements in exchange rates are partially mitigated by the natural, opposite effect that exchange rates have on our international operating costs and expenses.

We have a foreign currency management program with the objective of reducing the effect of exchange rate fluctuations on our operating results and forecasted revenues and expenses denominated in foreign currencies. We currently have cash flow hedges for the Euro, British Pound, Canadian Dollar and Australian Dollar related to a portion of our forecasted product revenues that qualify for hedge accounting treatment under U.S. GAAP. We do not seek hedge accounting treatment for our foreign currency forward contracts related to monetary assets and liabilities that impact our operating results. As of September 30, 2020, we held foreign exchange forward contracts that were designated as cash flow hedges with notional amounts totaling $966.6 million representing a net liability at fair value of $32.1 million on our condensed consolidated balance sheet.

Although not predictive in nature, we believe a hypothetical 10% threshold reflects a reasonably possible near-term change in exchange rates. Assuming that the September 30, 2020 exchange rates were to change by a hypothetical 10%, the fair value recorded on our condensed consolidated balance sheet related to our foreign exchange forward contracts that were designated as cash flow hedges as of September 30, 2020 would change by approximately $96.7 million. However, since these contracts hedge a specific portion of our forecasted product revenues denominated in certain foreign currencies, any change in the fair value of these contracts is recorded in “Accumulated other comprehensive loss” on our condensed consolidated balance sheet and is reclassified to earnings in the same periods during which the underlying product revenues affect earnings. Therefore, any change in the fair value of these contracts that would result from a hypothetical 10% change in exchange rates would be entirely offset by the change in value associated with the underlying hedged product revenues

~~resulting in no impact on our future anticipated earnings and cash flows with respect to the hedged portion of our forecasted product revenues.~~

~~Equity Price Risk~~

Information required by this ~~section~~item is incorporated by reference from the discussion in Part II, Item 7A, “Quantitative and Qualitative Disclosures About Market Risk,” of our Annual Report on Form 10-K for the ~~“Strategic Investments” section of this Part I, Item 2, “Management’s Discussion and Analysis of Financial Condition and Results of Operations.”~~year ended December 31, 2020, which was filed with the SEC on February 11, 2021.

Item 4. Controls and Procedures

Evaluation of Disclosure Controls and Procedures

Our management (under the supervision and with the participation of our chief executive officer and chief financial officer), after evaluating the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended) as of the end of the period covered by this Quarterly Report on Form 10-Q, has concluded that, based on such evaluation, as of ~~September 30, 2020~~March 31, 2021 our disclosure controls and procedures were effective and designed to provide reasonable assurance that the information required to be disclosed is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms. In designing and evaluating our disclosure controls and procedures, our management recognized that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives, and our management necessarily was required to apply its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

Changes in Internal Controls Over Financial Reporting

No change in our internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Securities Exchange Act of 1934, as amended) occurred during the three months ended ~~September 30, 2020~~March 31, 2021 that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

PART II. Other Information

Item 1. Legal Proceedings

We are not currently subject to any material legal proceedings.

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Item 1A. Risk Factors

Information regarding risk factors appears in Part I, Item 1A. “Risk Factors” of our Annual Report on Form 10-K for the year ended December 31, ~~2019,~~2020, which was filed with the SEC on February ~~13, 2020.~~11, 2021. There have been no material changes from the risk factors previously disclosed in the Annual Report on Form 10-K, except as discussed in Part II, Item 1A. “Risk Factors” in our Quarterly Report on Form 10-Q for the quarter ended March 31, 2020, which was filed with the SEC on May 1, 2020 and our Quarterly Report on Form 10-Q for the quarter ended June 30, 2020, which was filed with the SEC on July 31, 2020 and is being updated below.

~~We are subject to risks associated with the spread of COVID-19.~~

COVID-19 has broadly affected the global economy, resulted in significant travel and work restrictions in many regions and has put a significant strain on healthcare resources. COVID-19 has had, and we expect it will continue to have, an impact on our operations and an impact on the operations of our collaborators, third-party contractors and other entities, including governments, governmental agencies and payors, with which we interact. To date, the most significant effect on our business operations has been the requirement that a majority of our employees work remotely. We have re-initiated enrollment and dosing in all of our ongoing clinical trials and initiated new clinical trials despite some earlier temporary pauses to enrollment and dosing caused by COVID-19.

We continue to monitor local COVID-19 trends and government guidance for each of our site locations and have begun to re-open certain of our sites utilizing a phased, site-specific approach. There can be no assurance that these re-openings will continue or that, due to additional waves of increased infections, updated government guidance or other considerations, we will not be required to temporarily close or ramp-down sites that had re-opened or to pause enrollment and dosing at clinical trial sites. Any site closure or pause of a clinical trial could harm our operations and delay the development of our product candidates.

In the future, the economic impacts of the COVID-19 pandemic could affect our business directly or indirectly, including potentially affecting the net prices for our products through changes in our payor mix as a result of increased unemployment in the United States or increased pressure on healthcare costs. The effects on our research, development, manufacturing and commercialization activities will be dependent on, among other things, the severity and duration of the COVID-19 pandemic, and any worsening of the global economic environment as a result thereof, as well as the impact of the pandemic on our third-party manufacturers, suppliers, distributors, subcontractors and customers. While the ultimate impact of COVID-19 on our business is highly uncertain, any negative impacts that materialize could materially adversely affect our operations, financial performance and stock price. Any negative impacts of COVID-19, alone or in combination with others, could exacerbate other risk factors discussed in Part I, “Item 1A. Risk Factors” in our Annual Report on Form 10-K for the year ended December 31, 2019. The full extent to which the COVID-19 pandemic will negatively affect our operations, financial performance and stock price will depend on future developments that are highly uncertain and cannot be predicted, including the scope and duration of the pandemic and actions taken by governmental authorities and other third parties in response to the pandemic.10-K.

SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q and, in particular, our Management’s Discussion and Analysis of Financial Condition and Results of Operations set forth in Part I, Item 2, contain a number of forward-looking statements. Forward-looking statements ~~within the meaning~~are not purely historical and may be accompanied by words such as “anticipates,” “may,” “forecasts,” “expects,” “intends,” “plans,” “potentially,” “believes,” “seeks,” “estimates,” and other words and terms of ~~Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended, including~~similar meaning. Such statements ~~regarding:~~may relate to:

•our expectations regarding the amount of, timing of, and trends with respect to our financial performance, including revenues, costs and expenses and other gains and losses, including those related to net product revenues;

•our expectations regarding the effect of COVID-19 on, among other things, our financial performance, liquidity, business and operations, including manufacturing, supply chain, research and development activities and pipeline programs;

•our expectations regarding clinical trials, development timelines, regulatory authority filings, submissions and potential approvals and label expansions for ivacaftor, lumacaftor, tezacaftor, elexacaftor, and any combination regimen;

•our ability to obtain reimbursement for our medicines in the U.S. and ex-U.S. markets and our ability to launch, commercialize and market our medicines or any of our other drug candidates for which we obtain regulatory approval;

•our expectations regarding the timing and structure of clinical trials of our drugs, drug candidates and other pipeline programs and the expected timing of our receipt of data from our ongoing and planned clinical trials;

•the data that will be generated by ongoing and planned clinical trials and the ability to use that data to advance compounds, continue development or support regulatory filings;

•our beliefs regarding the support provided by clinical trials and preclinical and nonclinical studies of our drug candidates and other pipeline programs for further investigation, clinical trials or potential use as a treatment;

•our beliefs regarding the number of people with CF and those potentially eligible for our medicines;

•our expectations regarding the potential benefits and commercial potential of our product candidates, including the potential approach to treating specific diseases;

•our plan to continue investing in our research and development programs, including anticipated timelines for our programs, and our strategy to develop our pipeline programs, alone or with third party-collaborators;

•the potential future benefits of our acquisitions and ~~collaborations;~~collaborations, including our CTX001 collaboration with CRISPR;

•the establishment, development and maintenance of collaborative relationships, including potential milestone payments or other obligations;

•potential business development activities, including the identification of potential collaborative partners or acquisition targets;

•the timing of the potential closing of the transaction contemplated by the A&R JDCA, including satisfaction of closing conditions, and the future activities of the parties pursuant to the A&R JDCA;

•our expectation that we will record the $900.0 million upfront payment to CRISPR as a research and development expense upon the closing of the transaction contemplated by the A&R JDCA;

•potential fluctuations in foreign currency exchange rates;

•our expectations regarding our provision for or benefit from income taxes and the utilization of our deferred tax assets, including the impact of the Coronavirus Aid, Relief and Economic Security Act;

•our ability to use our research programs to identify and develop new drug candidates to address serious diseases and significant unmet medical needs; and

•our liquidity and our expectations regarding the possibility of raising additional capital.

~~Any~~Forward-looking statements are subject to certain risks, uncertainties, or ~~all of our forward-looking statements in this Quarterly Report on Form 10-Q may turn out~~other factors that are difficult to ~~be wrong. There are a number of assumptions, risks,~~predict and ~~uncertainties, known or unknown, which~~ could cause actual events or results to differ materially from those indicated byin any such statements.These risks, uncertainties, and other factors include, but are not limited to, those described in our ~~forward-looking statements, including the risks and uncertainties described under~~ “Risk Factors” in Item 1A of our Annual Report on Form 10-K for the year ended December 31, ~~2019,~~2020, which was filed with the SEC on February ~~13, 2020,~~11, 2021, and those described from time to time in our ~~Quarterly Report on Form 10-Q for the quarter ended March 31, 2020, which was~~future reports filed with the ~~SEC on May 1, 2020, our Quarterly Report on Form 10-Q for the quarter ended June 30, 2020, which was filed with the SEC on July 31, 2020~~Securities and in this Quarterly Report on Form 10-Q. These are factors and uncertainties that we think could cause our actual results to differ materially from expected results. Other factors and uncertainties besides those listed there could also adversely affect us.Exchange Commission.

Without limiting the foregoing, the words “believes,” “anticipates,” “plans,” “intends,” “expects,” “could,” “may,” “potential,” “will,” “estimate” and similar expressions are intended to identify forward-looking statements. TheAny such forward-looking statements ~~contained herein represent~~are made on the basis of our ~~estimate only~~views and assumptions as of the date of ~~this~~the filing and ~~should~~are not ~~be relied upon~~estimates of future performance. Except as ~~representing our estimate as of any subsequent date. While~~required by law, we ~~may elect to update these forward-looking statements at some point in the future, we specifically disclaim any~~undertake no obligation to ~~do so~~publicly update any forward-looking statements. The reader is cautioned not to ~~reflect actual results, changes in assumptions or changes in other factors affecting~~place undue reliance on any such ~~forward-looking~~ statements.

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Item 2. Unregistered Sales of Equity Securities and Use of Proceeds

Issuer Repurchases of Equity Securities

In ~~July 2019,~~November 2020, our Board of Directors approved a share repurchase program (the ~~“2019~~“2020 Share Repurchase Program”), pursuant to which we ~~are~~were authorized to repurchase up to $500.0 million of our common stock ~~between August 1, 2019 and~~by December 31, ~~2020.~~2022. As of March 31, 2021, we had repurchased the entire $500.0 million of common stock that was authorized under the 2020 Share Repurchase Program. The table set forth below shows repurchases of securities by us during the three months ended ~~September 30, 2020~~March 31, 2021 under our ~~2019~~2020 Share Repurchase Program.

Period Total Number
of Shares Purchased Average Price
Paid per Share Total Number of Shares
Purchased as Part of
Publicly Announced
Plans or Programs (1) Approximate Dollar Value of Shares that May Yet be Purchased Under the Plans or Programs (1)
July 1, 2020 to July 31, 2020 — $— — $164,001,989
August 1, 2020 to August 31, 2020 310,562 $270.48 310,562 $80,002,649
September 1, 2020 to September 30, 2020 92,157 $260.42 92,157 $56,003,011
Total 402,719 $268.17 402,719 $56,003,011


Period	Total Number of Shares Purchased	Average Price Paid per Share		Total Number of Shares Purchased as Part of Publicly Announced Plans or Programs (1)	Approximate Dollar Value of Shares that May Yet be Purchased Under the Plans or Programs (1)
January 1, 2021 to January 31, 2021	—	$	—	—	$	424,912,410
February 1, 2021 to February 28, 2021	1,988,941	$	213.64	1,988,941	$	—
March 1, 2021 to March 31, 2021	—	$	—	—	$	—
Total	1,988,941	$	213.64	1,988,941	$	—

(1) Under our ~~2019~~2020 Share Repurchase Program, we ~~are~~were authorized to purchase shares from time to time through open market or privately negotiated transactions. Such purchases ~~may be~~were made pursuant to Rule 10b5-1 plans or other means as determined by our management and in accordance with the requirements of the Securities and Exchange Commission.

Item 5. Other Information

As previously announced, Paul Silva, our Senior Vice President and Chief Accounting Officer, retired from the Company on April 30, 2021.

Effective May 1, 2021, Kristen Ambrose, 45, will become our Chief Accounting Officer. Ms. Ambrose has been our Senior Vice President, Accounting, Tax, Treasury, Strategic Sourcing and Corporate Services since March 2021. From February 2003 until she joined the Company, Ms. Ambrose held roles of increasing responsibility at Boston Scientific Corporation, a medical device company, most recently as Vice President of Finance and Controller of the Global Endoscopy Division from July 2019 to March 2021 and as Vice President of Global Internal Audit from February 2017 to June 2019.

Table of Contents

Prior to Boston Scientific Corporation, Ms. Ambrose served as an accountant at Ernst & Young LLP. She received her B.S. from the University of Virginia and is a Certified Public Accountant.

Item 6. Exhibits


Exhibit Number			Exhibit Description
~~10.1~~			~~Credit Agreement, dated as of September 18, 2020, by and among Vertex Pharmaceuticals Incorporated, Bank of America, N.A. and the other lenders party thereto.~~
31.1			Certification of the Chief Executive Officer under Section 302 of the Sarbanes-Oxley Act of 2002.
31.2			Certification of the Chief Financial Officer under Section 302 of the Sarbanes-Oxley Act of 2002.
32.1			Certification of the Chief Executive Officer and the Chief Financial Officer under Section 906 of the Sarbanes-Oxley Act of 2002.
101.INS			XBRL Instance - the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document.
101.SCH			XBRL Taxonomy Extension Schema
101.CAL			XBRL Taxonomy Extension Calculation
101.LAB			XBRL Taxonomy Extension Labels
101.PRE			XBRL Taxonomy Extension Presentation
101.DEF			XBRL Taxonomy Extension Definition
104			Cover Page Interactive Data File––the cover page interactive data file does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document.

4136

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.


	Vertex Pharmaceuticals Incorporated

~~October~~April 30, ~~2020~~2021	By:	/s/ Charles F. Wagner, Jr.
		Charles F. Wagner, Jr.
		Executive Vice President, Chief Financial Officer (principal financial officer and duly authorized officer)

4237


	As of September 30, 2020
	Unrecognized Expense		Weighted-average Recognition Period
	(in thousands)		(in years)
Type of award:
Restricted stock units (including PSUs)	$	487,254	2.06
Stock options	$	76,261	1.95
ESPP share issuances	$	3,265	0.44


	Options Outstanding				Options Exercisable
Range of Exercise Prices	Number Outstanding	Weighted-average Remaining Contractual Life	Weighted-average Exercise Price		Number Exercisable	Weighted-average Exercise Price
	(in thousands)	(in years)	(per share)		(in thousands)	(per share)
$36.28–$40.00	62	1.09	$	38.06	62	$	38.06
$40.01–$60.00	157	1.98	$	47.13	157	$	47.13
$60.01–$80.00	105	3.49	$	74.82	104	$	74.82
$80.01–$100.00	1,029	5.66	$	88.91	919	$	89.20
$100.01–$120.00	129	4.39	$	109.27	128	$	109.21
$120.01–$140.00	282	4.98	$	129.42	281	$	129.43
$140.01–$160.00	740	7.36	$	155.49	369	$	155.41
$160.01–$180.00	599	7.76	$	168.34	282	$	165.74
$180.01–$200.00	1,252	8.14	$	185.31	422	$	184.85
$200.01–$286.27	23	9.67	$	286.27	23	$	286.27
Total	4,378	6.63	$	140.26	2,747	$	123.22