| Artist | Album | Song Title | Start/Stop | Scene |
| 2x01 - The Enemy Walks In: |
| Daniel Lenz | | | 00:18:39 - 00:19:25 (DVD) | Sydney rescues Vaughn. |
| Rosie Thomas | When We Were Small | | 00:26:51 - 00:28:59 (DVD) | Will tells Sydney about his last day at work. |
| Gemma Hayes | Night on My Side | | 00:37:06 - 00:38:27 (DVD) | Sydney preparing for Emily's funeral. |
| 2x02 - Trust Me: |
| Catie Curtis | A Crash Course in Roses | | 00:27:00 - 00:28:15 (DVD) | Will offers to help Francie. |
| Supreme Beings of Leisure | Divine Operating System | | 00:32:52 - 00:34:13 (DVD) | At the club in Helsinki. |
| Bob Dylan | Blood on the Tracks | | 00:37:57 - 00:41:13 (DVD) | Sydney confronts her mother. |
| 2x03 - Cipher: |
| Mary Lorson | Saint Low | | 00:14:10 - 00:15:15 (DVD) | Sydney tells Will about Vaughn. |
| 2x04 - Dead Drop: |
| Innocence Mission | Small Planes | | 00:10:16 - 00:11:41 (DVD) | Sydney and Francie / Sydney and Will talk over breakfast. |
| Michelle Featherstone | Fallen Down | | 00:38:55 - 00:41:10 (DVD) | Irina is moved. |
| 2x05 - The Indicator: |
| Zero 7 | Simple Things | | 00:02:06 - 00:03:05 (DVD) | Sydney visits her mother's cell. |
| Cornershop | When I Was Born for the 7th Time | | 00:09:39 - 00:10:22 (DVD) | Sydney, Will and Francie at the restaurant. |
| Robin Thicke | A Beautiful World | | 00:10:22 - 00:11:50 (DVD) | Sydney and Will dance, Jack comes to the restaurant. |
| Beck | Sea Change | | 00:24:23 - 00:25:39 (DVD) | Will and Sydney have a picnic. |
| Miriam Gauci | | Verdi's Canzone del Salce - Ave Maria | 00:28:36 - 00:29:31 (DVD) | Sloane takes a shower. |
| Joni Mitchell | Blue | | 00:37:47 - 00:41:06 (DVD) | At the end of the episode. |
| 2x06 - Salvation: |
| Violent Femmes | Violent Femmes | | 00:07:59 - 00:09:26 (DVD) | Sydney and Will talk at Francie's. |
| Gus | Uncivilized Love | | 00:13:34 - 00:14:00 (DVD) | Vaughn and Will meet. |
| Andy Hunter | Exodus | | 00:16:55 - 00:17:57 (DVD) | Jack and Sydney in the hospital. |
| Kim Richey | Rise | | 00:29:45 - 00:32:10 (DVD) | Vaughn and Sydney waiting for the test results. |
| 2x07 - The Counteragent: |
| Debbie Weisberg | | | 00:04:46 - 00:06:13 (DVD) | Sydney and Will help Francie at the restaurant. |
| Yo-Yo Ma | Appalachian Journey | | 00:08:27 - 00:11:29 (DVD) | Sydney visits Vaughn at the hospital. |
| Peter Gabriel | Up | | 00:32:37 - 00:35:20 (DVD) | Sydney sees Sloane's empty office. |
| Sheryl Crow | Tuesday Night Music Club | | 00:37:50 - 00:40:48 (DVD) | Sydney and Vaughn talk about Alice. |
| 2x08 - Passage (1): |
| The Creedence Clearwater Revival | Green River | | 00:00:50 - 00:01:28 (DVD) | Sark and Sydney take a drive before work. |
| Josh Canova | Common Divide | | 00:18:13 - 00:19:58 (DVD) | Will and Syd talk at home. |
| U2 | All That You Can't Leave Behind | | 00:38:22 - 00:40:14 (DVD) | At the end of the episode. |
| 2x09 - Passage (2): |
| The Rolling Stones | Emotional Rescue | | 00:40:21 - 00:41:14 (DVD) | Mini golf with Will and Francie. |
| 2x10 - The Abduction: |
| Chumbawamba | Readymades | | 00:20:09 - 00:22:03 (DVD) | Syd and Will bump into Vaughn and Alice at the bar. |
| Johann Sebastian Bach | | | 00:30:41 - 00:34:31 (DVD) | Syd and Marshall on their mission. |
| Dar Williams | Beauty Live | | 00:35:11 - 00:36:37 (DVD) | Sydney says goodbye to Marshall back in LA. |
| Boomkat | Boomkatalog One | | 00:37:15 - 00:37:45 (DVD) | Francie's surprise birthday party. |
| 2x11 - A Higher Echelon: *(Additional music info in episode details) |
| Jude | | | 00:04:27 - 00:05:48 (DVD) | Sydney tells Francie about Vaughn. |
| Sammy Hagar | Ten 13 | | 00:27:38 - 00:27:57 (DVD) | Marshall outwits Suit and Glasses. |
| Kinky | Kinky | | 00:32:34 - 00:34:28 (DVD) | Syd and Dixon at a techno club. |
| Matthew Good Band | | | 00:38:16 - 00:39:27 (DVD) | Marshall returns to SD-6. |
| 2x12 - The Getaway: |
| No Doubt | Rock Steady | | 00:16:17 - 00:17:58 (DVD) | Sydney strips for the metal detector. |
| Beck | Sea Change | | 00:35:55 - 00:37:45 (DVD) | Francie and Sydney talk and go for cocktails. |
| Charles Gounod | | | 00:39:06 - 00:40:13 (DVD) | Sloane and Emily reunite. |
| 2x13 - Phase One: |
| AC/DC | Back In Black | | 00:00:00 - 00:01:30 (DVD) | Sydney struts in her lingerie. |
| Lenny Kravitz | 5 | | 00:04:13 - 00:05:00 (DVD) | Sydney jogs through the park. |
| Groove Armada | Love Box | | 00:17:08 - 00:18:26 (DVD) | Francie and Will kiss. |
| Bill Withers | Greatest Hits | | 00:19:18 - 00:19:58 (DVD) | Will and Francie tell Syd they made out. |
| 2x14 - Double Agent: |
| The Cars | The Cars | | 00:12:01 - 00:13:35 (DVD) | Sydney climbs out of the pool. |
| Coldplay | A Rush of Blood to the Head | God Put a Smile Upon Your Face | 00:38:35 - 00:40:50 (DVD) | Syd makes dinner for Vaughn. |
| 2x15 - A Free Agent: |
| Jimmy Eat World | Jimmy Eat World | | 00:00:56 - 00:02:14 (DVD) | Sydney and Vaughn in bed. |
| Evan Olson | Red | | 00:07:41 - 00:08:27 (DVD) | Sydney in her graduation gown. |
| The Vines | Highly Evolved | | 00:31:50 - 00:33:20 (DVD) | Vaughn bullying in a bar. |
| 2x16 - Firebomb: |
| Duncan Sheik | Daylight | | 00:12:13 - 00:13:35 (DVD) | Francie tells Syd "she's been acting weird". |
| David Gray | A New Day at Midnight | | 00:37:55 - 00:40:31 (DVD) | Vaughn comforts Sydney. |
| 2x17 - A Dark Turn: |
| LaTour | LaTour | | 00:12:58 - 00:15:33 (DVD) | Irina in a Bangkok nightclub. |
| Lucinda Williams | World Without Tears | | 00:30:22 - 00:31:26 (DVD) | Sydney spies on Vaughn at the bar. |
| 2x18 - Truth Takes Time: |
| Josh Kelley | For the Ride Home | | 00:23:07 - 00:24:02 (DVD) | Francie gives Vaughn a tie. |
| Eastmountainsouth | Eastmountainsouth | | 00:38:40 - 00:40:23 (DVD) | Sydney and Vaughn in bed. |
| 2x19 - Endgame: |
| Luce | Luce | | 00:06:01 - 00:07:20 (DVD) | Syd gives Vaughn the middle drawer. |
| Turin Brakes | Ether Song | | 00:15:18 - 00:16:47 (DVD) | Dixon and Diane discuss their future. |
| The Breeders | Last Splash | | 00:19:27 - 00:21:04 (DVD) | Sydney disguises herself as a sorority girl. |
| Bering Strait | Bering Strait | | 00:23:10 - 00:24:34 (DVD) | Sydney in Moscow. |
| 2x20 - Countdown: |
| Lizzie West | Holy Road: Freedom Songs | | 00:01:41 - 00:03:09 (DVD) | Funeral at Dixon's. |
| Kinky | Kinky | | 00:14:47 - 00:15:48 (DVD) | Fight in the club. |
| Aretha Franklin | 30 Greatest Hits | You're All I Need to Get By | 00:37:18 - 00:39:02 (DVD) | Sydney and Vaughn eat ice cream. |
| 2x21 - Second Double: |
| Macy Gray | The Trouble with Being Myself | | 00:00:58 - 00:02:12 (DVD) | Syd and Vaughn mix business with pleasure. |
| The Lawyer | I Wanna Mmm | | 00:17:13 - 00:18:57 (DVD) | At the sex club. |
| Glendooz | | | 00:36:03 - 00:36:43 (DVD) | Vaughn pretends to be drunk. |
| 2x22 - The Telling: |
| Fleetwood Mac | The Dance | | 00:04:27 - 00:05:45 (DVD) | Sydney and Vaughn discuss vacation. |