The soundtrack for The Dangerous Lives of Altar Boys finds members of Rage Against the Machine (Brad Wilk) and Queens of the Stone Age (Joshua Homme and Nick Oliveri) performing music that doesn't sound anything like the bands that people identify them with. Much of the disc is devoted to instrumental film music; Homme and Marco Beltrami do the composing, while Wilk, Homme, and Oliveri are among the main people who play the music.

• 1 The Atomic Trinity
• 2 The Atomic Trinity Vs. Heaven's Devils
• 3 The Empty House
• 4 The Couch
• 5 Hanging (aka Ramble Off)
• 6 Margie's Confession
• 7 Atomic Trinity Vs. Heaven's Devils, Round II
• 8 St. Agatha
• 9 On The Road Again
• 10 Francis And Margie
• 11 Dead Dog, Part II
• 12 Skeleton Boy Is Born
• 13 Do For The Others
• 14 Story Of The Fish
• 15 For The Gods/Act Like Cougars
• 16 Torn Apart
• 17 Someone Is Coming
• 18 Eulogy
• 19 Stoned
• 20 All The Same