Marketable securities (Details) (USD $) | 6 Months Ended | 12 Months Ended | |
Sep. 30, 2013 | Sep. 30, 2012 | Mar. 31, 2013 | Jun. 30, 2013 |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Total available-for-sale debt securities: Estimated fair value | $2,126,084,000 | ' | $2,050,518,000 | ' |
Total available-for-sale debt securities: Gains in accumulated other comprehensive income | 4,431,000 | ' | 7,206,000 | ' |
Total available-for-sale debt securities: Losses in accumulated other comprehensive income | -6,042,000 | ' | -2,966,000 | ' |
Proceeds from sales of available-for-sale debt securities | 613,300,000 | 1,100,000,000 | ' | ' |
Gross realized gains on sales of available-for-sale debt securities | 500,000 | 1,000,000 | ' | ' |
Net unrealized holding gains (losses) on available-for-sale debt securities | 1,600,000 | ' | 4,200,000 | ' |
Investment in Ironwood Pharmaceuticals, Inc. | 24,700,000 | ' | 38,100,000 | ' |
Investment in Trevena, Inc. | ' | ' | ' | 30,000,000 |
Contractual maturities of available-for-sale debt securities, fair value [Abstract] | ' | ' | ' | ' |
Within one year | 757,357,000 | ' | ' | ' |
1-5 years | 1,329,877,000 | ' | ' | ' |
5-10 years | 4,402,000 | ' | ' | ' |
After 10 years | 34,448,000 | ' | ' | ' |
Total available-for-sale debt securities: Estimated fair value | 2,126,084,000 | ' | 2,050,518,000 | ' |
Current [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, current | 757,357,000 | ' | 739,198,000 | ' |
Gains in accumulated other comprehensive income | 1,183,000 | ' | 1,445,000 | ' |
Losses in accumulated other comprehensive income | -164,000 | ' | -45,000 | ' |
Noncurrent [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, non-current | 1,368,727,000 | ' | 1,311,320,000 | ' |
Gains in accumulated other comprehensive income | 3,248,000 | ' | 5,761,000 | ' |
Losses in accumulated other comprehensive income | -5,878,000 | ' | -2,921,000 | ' |
Municipal Bonds and Notes [Member] | Current [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, current | 11,727,000 | ' | 34,025,000 | ' |
Gains in accumulated other comprehensive income | 11,000 | ' | 34,000 | ' |
Losses in accumulated other comprehensive income | 0 | ' | 0 | ' |
Municipal Bonds and Notes [Member] | Noncurrent [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, non-current | 7,895,000 | ' | 12,852,000 | ' |
Gains in accumulated other comprehensive income | 24,000 | ' | 37,000 | ' |
Losses in accumulated other comprehensive income | 0 | ' | 0 | ' |
Government Agency Bonds [Member} | Current [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, current | 75,462,000 | ' | 87,227,000 | ' |
Gains in accumulated other comprehensive income | 169,000 | ' | 125,000 | ' |
Losses in accumulated other comprehensive income | -1,000 | ' | -10,000 | ' |
Government Agency Bonds [Member} | Noncurrent [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, non-current | 178,710,000 | ' | 186,577,000 | ' |
Gains in accumulated other comprehensive income | 184,000 | ' | 434,000 | ' |
Losses in accumulated other comprehensive income | -226,000 | ' | -19,000 | ' |
Commercial Paper [Member] | Current [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, current | 82,357,000 | ' | 144,293,000 | ' |
Gains in accumulated other comprehensive income | 0 | ' | 0 | ' |
Losses in accumulated other comprehensive income | 0 | ' | 0 | ' |
Commercial Paper [Member] | Noncurrent [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, non-current | 2,850,000 | ' | ' | ' |
Gains in accumulated other comprehensive income | 0 | ' | ' | ' |
Losses in accumulated other comprehensive income | 0 | ' | ' | ' |
Certificates of Deposit [Member] | Current [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, current | 99,966,000 | ' | 47,977,000 | ' |
Gains in accumulated other comprehensive income | 22,000 | ' | 0 | ' |
Losses in accumulated other comprehensive income | -15,000 | ' | -2,000 | ' |
Certificates of Deposit [Member] | Noncurrent [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, non-current | 3,000,000 | ' | 22,999,000 | ' |
Gains in accumulated other comprehensive income | 0 | ' | 0 | ' |
Losses in accumulated other comprehensive income | 0 | ' | 0 | ' |
Corporate Bonds [Member] | Current [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, current | 487,845,000 | ' | 425,676,000 | ' |
Gains in accumulated other comprehensive income | 981,000 | ' | 1,286,000 | ' |
Losses in accumulated other comprehensive income | -148,000 | ' | -33,000 | ' |
Corporate Bonds [Member] | Noncurrent [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, non-current | 1,143,934,000 | ' | 1,084,194,000 | ' |
Gains in accumulated other comprehensive income | 3,040,000 | ' | 5,290,000 | ' |
Losses in accumulated other comprehensive income | -5,652,000 | ' | -2,150,000 | ' |
Auction Rate Securities [Member] | Noncurrent [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, non-current | 3,198,000 | ' | 3,198,000 | ' |
Gains in accumulated other comprehensive income | 0 | ' | 0 | ' |
Losses in accumulated other comprehensive income | 0 | ' | -752,000 | ' |
Variable Rate Demand Note [Member] | Noncurrent [Member] | ' | ' | ' | ' |
Schedule of Available-for-sale Securities [Line Items] | ' | ' | ' | ' |
Estimated fair value, non-current | 29,140,000 | ' | 1,500,000 | ' |
Gains in accumulated other comprehensive income | 0 | ' | 0 | ' |
Losses in accumulated other comprehensive income | $0 | ' | $0 | ' |