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Disc1
| 1 | Main Titles | Ramin Djawadi | 2:29 |
| 2 | Strings of Prisoners | Ramin Djawadi | 1:27 |
| 3 | Inking the Plan | Ramin Djawadi | 2:37 |
| 4 | Save a Brother's Life | Ramin Djawadi | 1:52 |
| 5 | In the Yard | Ramin Djawadi | 1:45 |
| 6 | T-Bag's Coming for Dinner | Ramin Djawadi | 1:43 |
| 7 | Sucre's Dilemma | Ramin Djawadi | 2:26 |
| 8 | Sarah & Michael | Ramin Djawadi | 1:43 |
| 9 | Abruzzi Is the Ticket | Ramin Djawadi | 1:57 |
| 10 | In the Tunnels | Ramin Djawadi | 2:56 |
| 11 | Unconditional | Ramin Djawadi | 2:19 |
| 12 | Conspiracy | Ramin Djawadi | 2:41 |
| 13 | Sarah | Ramin Djawadi | 2:44 |
| 14 | C-Note | Ramin Djawadi | 2:07 |
| 15 | An In-Be-Tweener | Ramin Djawadi | 3:12 |
| 16 | Prison Break | Ramin Djawadi | 3:33 |
| 17 | The Manhunt Begins | Ramin Djawadi | 2:15 |
| 18 | Special Agent Mahone | Ramin Djawadi | 1:23 |
| 19 | Veronica Is Murdered | Ramin Djawadi | 1:49 |
| 20 | Linc & LJ | Ramin Djawadi | 2:04 |
| 21 | Stand-Off | Ramin Djawadi | 1:58 |
| 22 | Cat & Mouse | Ramin Djawadi | 1:33 |
| 23 | (Classified) | Ramin Djawadi | 2:02 |
| 24 | Remorse | Ramin Djawadi | 2:30 |
| 25 | Origami | Ramin Djawadi | 1:03 |
| 26 | Escape Is Just the Beginning | Ramin Djawadi | 2:11 |
| 27 | Panama | Ramin Djawadi | 1:21 |
| 28 | Maricruz | Ramin Djawadi | 1:09 |
| 29 | Execution | Ramin Djawadi | 1:49 |
| 30 | Trouble in Paradise | Ramin Djawadi | 1:18 |
| 31 | Sona | Ramin Djawadi | 1:35 |