| Artist | Album | Song Title | Start/Stop | Scene |
| 1x01 - Truth Be Told: |
| The Stereo MCs | Deep Down & Dirty | | (TV) | Sydney in the garage scene. |
| Vertical Horizon | Everything You Want | | 00:02:06 - 00:03:14 (DVD) | Before Danny proposes. |
| Gus | Word of Mouth Parade | | 00:04:01 - 00:05:20 (DVD) | Sydney and Francine talk about the engagement. |
| Supreme Beings of Leisure | Supreme Beings of Leisure | | 00:06:44 - 00:08:40 (DVD) | Sydney arrives at SD-6 |
| The Cranberries | Wake Up and Smell the Coffee | | 00:13:25 - 00:15:06 (DVD) | Sydney and Danny at home. |
| Cat Stevens | | | 00:17:01 - 00:19:38 (DVD) | Sydney remembering her recruitment. |
| Peter Gabriel | Hit | | 00:34:25 - 00:37:11 (DVD) | During the funeral. |
| Sinéad O'Connor | Faith and Courage | | 00:55:23 - 00:56:55 (DVD) | Sydney delivers the artifact to Sloan. |
| Vertical Horizon | Everything You Want | | 00:59:33 - 01:02:56 (DVD) | At the end of the episode. |
| 1x02 - So It Begins: |
| Roland Gift | Roland Gift | | 00:08:49 - 00:10:05 (DVD) | Sydney moving in. |
| Kate Bush | The Sensual World | | 00:28:08 - 00:29:25 (DVD) | Sydney coming home. |
| 1x03 - Parity: |
| Bill Bonk | Eveningshade | | 00:04:04 - 00:06:19 (DVD) | Sydney and Francie talk about Sydney's dad. |
| Miranda Lee Richards | The Herethereafter | | 00:11:04 - 00:12:02 (DVD) | Sydney and Will on the phone at her home. |
| Spookie Daly Pride | Marshmallow Pie | | 00:26:47 - 00:28:36 (DVD) | During the poker game at Sydney's. |
| Ryan Adams | Gold | | 00:28:36 - 00:31:03 (DVD) | Sydney and Will kiss. |
| 1x04 - A Broken Heart: |
| Nina Storey | Shades | | 00:09:32 - 00:10:24 (DVD) | Sydney and Francie eat Chinese food. |
| Bill Bonk | Eveningshade | | 00:12:08 - 00:12:42 (DVD) | Sydney talks to Will. |
| Sarah McLachlan | Surfacing | | 00:30:08 - 00:34:17 (DVD) | Sydney is stood up by her father and talks to Vaughn |
| 1x05 - Doppelgänger: |
| John Wesley Harding | Confessions of St. Ace | I'm Wrong About Everything | 00:21:38 - 00:22:53 (DVD) | Will & Francie plan their Halloween party. |
| Freestylers | Pressure Point | | 00:26:24 - 00:27:53 (DVD) | Sydney and Dixon talk at the party. |
| Leroy | Leroy | | 00:27:53 - 00:29:06 (DVD) | Francie and Will talk at the party. |
| 1x06 - Reckoning: |
| STARS | Nightsongs | | 00:04:16 - 00:06:42 (DVD) | Sydney is looking at old photos and Francie comes home. |
| Garbage | When I Grow Up | | 00:20:05 - 00:21:44 (DVD) | Sydney and Dixon at the art gallery. |
| Huffamoose | I Wanna Be Your Pants | | 00:26:53 - 00:28:27 (DVD) | At the club waiting for Charlie to perform. |
| Lisbeth Scott | State of Grace | | 00:35:56 - 00:37:38 (DVD) | At the funeral |
| 1x07 - Color-Blind: |
| The Pretenders | Pretenders | | 00:19:28 - 00:20:12 (DVD) | Sydney and Shepard leave the asylum |
| Jude | King of Yesterday | Everything's All Right (I Think It's Time) | 00:31:19 - 00:34:42 (DVD) | During Thanksgiving dinner. |
| Natalie Merchant | Motherland | | 00:39:20 - 00:41:40 (DVD) | At the end of the episode. |
| 1x08 - Time Will Tell: |
| Ivy | Long Distance | | 00:14:46 - 00:16:51 (DVD) | Will visits Sydney while she works on her paper. |
| 1x09 - Mea Culpa: |
| Smash Mouth | Astro Lounge | | 00:19:16 - 00:21:12 (DVD) | Sydney at the party in Tuscany. |
| Munkafust | Welcome to Playtime | | 00:24:26 - 00:24:38 (DVD) | Jack talks to Marshall. |
| Duncan Sheik | Duncan Sheik | | 00:31:01 - 00:32:18 (DVD) | Sydney and Francie talking about wedding dress shopping. |
| 1x10 - Spirit: |
| Klyph Black | | | 00:11:37 - 00:13:09 (DVD) | During the Boggle game. |
| Thunderball | Scorpio Rising | | 00:17:45 - 00:18:58 (DVD) | Sydney at the hotel. |
| Freedy Johnston | Right Between the Promises | | 00:30:39 - 00:31:41 (DVD) | Will asks about Vaughn's gift to Sydney. |
| 1x11 - The Confession: |
| DJ Teebee | Through The Eyes Of A Scorpion | | 00:24:02 - 00:25:43 (DVD) | Sydney and Dixon at the club. |
| Sting | Let Your Soul Be Your Pilot | | 00:29:50 - 00:31:41 (DVD) | Sydney cries at Will's house. |
| 1x12 - The Box (1): |
| Enya | Shepherd Moons | How Can I Keep From Singing? | 00:02:23 - 00:04:31 (DVD) | Sydney tries to deal with the truth about her mother. |
| Rob Zombie | American Made Music to Strip By | Dragula (Si Non Oscillas, Noli Tintinnare Mix) | 00:07:56 - 00:08:41 (DVD) | Cole takes over SD-6. |
| Oscillatios vs Mukunga Umburu | | | 00:40:21 - 00:41:30 (DVD) | Cole and his team run to the vault. |
| 1x13 - The Box (2): |
| Jesse Harris | Crooked Lines | | 00:15:52 - 00:17:53 (DVD) | Will tells Francie about the story he is writing. |
| Fleetwood Mac | Rumours | | 00:40:01 - 00:42:54 (DVD) | At the end of the episode. |
| 1x14 - The Coup: |
| Norah Jones | Come Away with Me | | 00:09:06 - 00:11:13 (DVD) | Francie and Charly tell Sydney they plan to go to Vegas. |
| Chantal Kreviazuk | Under These Rocks and Stones | | 00:35:49 - 00:37:40 (DVD) | Sydney comforts Francie. |
| 1x15 - Page 47: |
| John Mayer | Room for Squares | | 00:03:32 - 00:04:56 (DVD) | Jenny and Will talk about the award. |
| Smashing Pumpkins | Pisces Iscariot | | 00:07:32 - 00:09:17 (DVD) | Sydney and Francie take their rings off. |
| Abra Moore | | | 00:23:05 - 00:23:33 (DVD) | Emily calls Sydney to invite to come over for dinner. |
| Norah Jones | Come Away with Me | | 00:27:04 - 00:27:58 (DVD) | Francie reads her thank you letter to Sydney. |
| 1x16 - The Prophecy: |
| Bill Bonk | Spaghetti Western | | 00:11:21 - 00:12:17 (DVD) | Sydney tells Will and Francie about a dream she had about a fortune teller. |
| Hathaway | | | 00:28:23 - 00:29:02 (DVD) | Francie getting ready for the basketball game with Will. |
| The Hives | Veni Vidi Vicious | Hate To Say I Told You So | 00:31:14 - 00:32:47 (DVD) | Sydney and Vaughn break into the Vatican. |
| Mint Royale | On the Ropes | | 00:39:21 - 00:41:01 (DVD) | Sydney meets Will and Francie at the bar. |
| 1x17 - Q & A: |
| Smash Mouth | Astro Lounge | | 00:28:52 - 00:30:02 (DVD) | Sydney's mission recap. |
| 1x18 - Masquerade: |
| Anonymous 4 | | | 00:02:20 - 00:04:13 (DVD) | Sydney climbing Mount Subasio. |
| Gigolo Aunts | Pacific Ocean Blues | | 00:10:42 - 00:11:23 (DVD) | Will, Francie and Sydney during breakfast. |
| Doves | Lost Souls | | 00:27:55 - 00:30:17 (DVD) | Sydney and Noah talk. |
| Depeche Mode | Exciter | | 00:39:30 - 00:42:38 (DVD) | Sydney and Noah in the cabin at the end of the episode. |
| 1x19 - Snowman: |
| Matt Beckler | Matt Beckler | | 00:06:32 - 00:07:31 (DVD) | Will and Francie discuss how to confront Sydney. |
| Jeff Buckley | Grace | Lover, You Should've Come Over | 00:20:24 - 00:22:00 (DVD) | Sydney and her father talk without words. |
| Paul Oakenfold | Bunkka | | 00:23:25 - 00:27:18 (DVD) | Marshall demonstrates his active noise control gadget and during the mission. |
| Hathaway | | | 00:30:38 - 00:31:09 (DVD) | Sydney feels bad she had to lie to Will and Francie again. |
| Gigolo Aunts | Pacific Ocean Blues | | 00:35:57 - 00:37:31 (DVD) | Noah calls Sydney from the plane. |
| 1x20 - The Solution: |
| Trickside | Trickside | | 00:20:55 - 00:21:04 (DVD) | Will tells his story to Abby. |
| Alison Krauss | New Favorite | | 00:25:52 - 00:27:45 (DVD) | Sydney tells Francie she slept with Noah. |
| 1x21 - Rendezvous: |
| Jacintha | Autumn Leaves: The Songs of Johnny Mercer | | 00:22:09 - 00:22:18 (DVD) | Sark at Khasinau's club. |
| Jennifer Garner | | | 00:24:16 - 00:26:31 (DVD) | Sydney singing at the nightclub. |
| Maren Ord | Waiting | | 00:37:52 - 00:40:02 (DVD) | Will and Sydney at the safehouse. |
| 1x22 - Almost Thirty Years: |
| Natalie Merchant | Ophelia | | 00:08:04 - 00:09:49 (DVD) | Sloane tells Emily that SD-6 is not part of the CIA. |
| Miriam Gauci | | Canzone Del Salce (Verdi's Otello) | 00:31:32 - 00:33:05 (DVD) | Sloane poisons Emily's wine. |
| The Chemical Brothers | Surrender | | 00:33:05 - 00:34:16 (DVD) | Sydney and Vaughn at the club in Taipei. |
| Overseer | Everything Louder Than Everything Else | | 00:38:53 - 00:39:54 (DVD) | Sydney and Vaughn trying to escape from the lab. |