| Song | Performer | Writer | Album | Year | |
| "3 Libras" | Vocals: Maynard James Keenan Guitar, Bass: Billy Howerdel Violin: Paz Lenchantin Viola: Luciano Lenchantin Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Mer de Noms | 2000 | |
| "A Stranger" | Vocals: Maynard James Keenan Guitar, Backing Vocals: Billy Howerdel Bass: Jeordie White Strings: The Section Quartet | Maynard James Keenan Billy Howerdel | Thirteenth Step | 2003 | |
"Annihilation" | Vocals: Maynard James Keenan Guitar, Piano, Keyboard, Programming: Billy Howerdel Keyboard, Programming: Danny Lohner | Original: Christopher Douglas, Matthew Borruso, Sothira Pheng Rearrangement: Maynard James Keenan Billy Howerdel | Emotive | 2004 | |
"Ashes to Ashes" | Vocals: Maynard James Keenan Guitar, Backing Vocals: Billy Howerdel Guitar: James Iha Bass: Matt McJunkins Drums: Josh Freese | Original: David Bowie Rearrangement: Maynard James Keenan Billy Howerdel | A Perfect Circle Live: Featuring Stone and Echo | 2013 | |
| "Blue" | Vocals: Maynard James Keenan Guitar, Backing Vocals: Billy Howerdel Bass: Jeordie White Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Thirteenth Step | 2003 | |
| "Brena" | Vocals: Maynard James Keenan Guitar, Bass, Backing Vocals: Billy Howerdel Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Mer de Noms | 2000 | |
| "By and Down" | Vocals: Maynard James Keenan Guitar, Piano, Backing Vocals: Billy Howerdel Bass: Matt McJunkins Drums: Jeff Friedl | Maynard James Keenan Billy Howerdel | Three Sixty | 2013 | |
| "By and Down the River" | Vocals: Maynard James Keenan Guitar,Keyboard: Billy Howerdel Bass: Matt McJunkins Drums: Jeff Friedl | Maynard James Keenan Billy Howerdel | Eat the Elephant | 2018 | |
| "The Contrarian" | Vocals: Maynard James Keenan Guitar, Bass, Keyboard: Billy Howerdel Drums: Jeff Friedl | Maynard James Keenan Billy Howerdel | Eat the Elephant | 2018 | |
| "Counting Bodies Like Sheep to the Rhythm of the War Drums" | Vocals: Maynard James Keenan Backing Vocals: Billy Howerdel Backing Vocals, Additional Instrumentation: Danny Lohner Drums, Electric Piano: Josh Eustis Saxophone: Jason Freese | Maynard James Keenan, Billy Howerdel, Arrangement: Danny Lohner, Keenan | Emotive | 2004 | |
| "Crimes" | Vocals: Maynard James Keenan Guitar: Billy Howerdel Bass: Jeordie White Drums: Josh Freese | Maynard James Keenan Billy Howerdel Josh Freese Jeordie White | Thirteenth Step | 2003 | |
| "Delicious" | Vocals: Maynard James Keenan Guitar, Bass, Keyboard: Billy Howerdel Drums: Jeff Friedl | Maynard James Keenan Billy Howerdel | Eat the Elephant | 2018 | |
"Diary of a Love Song" | Vocals: Maynard James Keenan Guitar, Backing Vocals: Billy Howerdel Guitar: James Iha Bass: Matt McJunkins Drums: Josh Freese | Original: Ozzy Osbourne, Randy Rhoads, Bob Daisley and Lee Kerslake, Robert Smith Rearrangement: Maynard James Keenan Billy Howerdel | A Perfect Circle Live: Featuring Stone and Echo | 2013 | |
| "Disillusioned" | Vocals: Maynard James Keenan Guitar, Bass, Keyboard: Billy Howerdel Drums: Jeff Friedl | Maynard James Keenan Billy Howerdel | Eat the Elephant | 2018 | |
| "DLB" | Piano: Billy Howerdel | Maynard James Keenan Billy Howerdel | Eat the Elephant | 2018 | |
| “Dog Eat Dog” | Vocals: Maynard James Keenan Guitar, Bass: Billy Howerdel Drums: Jeff Friedl | Angus Young, Malcolm Young, Bon Scott | “So Long, and Thanks for All the Fish” single | 2018 | |
| "The Doomed" | Vocals: Maynard James Keenan Guitar, Bass, Keyboard: Billy Howerdel Drums: Jeff Friedl | Maynard James Keenan Billy Howerdel | Eat the Elephant | 2018 | |
| "Eat the Elephant" | Vocals: Maynard James Keenan Guitar, Bass, Keyboard: Billy Howerdel Drums: Jeff Friedl | Maynard James Keenan Billy Howerdel | Eat the Elephant | 2018 | |
| "Feathers" | Vocals: Maynard James Keenan Guitar, Keyboard: Billy Howerdel Bass: Matt McJunkins Drums: Jeff Friedl | Maynard James Keenan Billy Howerdel | Eat the Elephant | 2018 | |
"Fiddle and the Drum" | Vocals: Maynard James Keenan | Original: Joni Mitchell Rearrangement: Maynard James Keenan | Emotive | 2004 | |
"Freedom of Choice" | Vocals, Guitar, Bass: Billy Howerdel Backing vocals: Maynard James Keenan, Drums: Josh Freese | Original: Gerald V. Casale, Mark Mothersbaugh Rearrangement: Billy Howerdel | Emotive | 2004 | |
| "Get the Lead Out" | Vocals: Maynard James Keenan Guitar, Bass, Keyboard: Billy Howerdel Drums: Jeff Friedl | Maynard James Keenan Billy Howerdel | Eat the Elephant | 2018 | |
"Gimmie, Gimmie, Gimmie" | Vocals: Maynard James Keenan Guitar, Harmonium Billy Howerdel Bass, Backing Vocals: Danny Lohner Drums: Josh Freese | Original: Greg Ginn Rearrangement: Maynard James Keenan | Emotive | 2004 | |
| Gravity" | Vocals: Maynard James Keenan Guitar, Backing Vocals: Billy Howerdel Guitar: Troy Van Leeuwen Bass: Jeordie White Drums: Josh Freese | Maynard James Keenan Billy Howerdel Josh Freese Troy Van Leeuwen Paz Lenchantin | Thirteenth Step | 2003 | |
| "The Hollow" | Vocals: Maynard James Keenan Guitar, Bass, Backing Vocals: Billy Howerdel Drums: Tim Alexander | Maynard James Keenan Billy Howerdel | Mer de Noms | 2000 | |
| "Hourglass" | Vocals: Maynard James Keenan Guitar, Bass, Keyboard: Billy Howerdel Drums: Jeff Friedl | Maynard James Keenan Billy Howerdel | Eat the Elephant | 2018 | |
"Imagine"
| Vocals, Piano: Maynard James Keenan Guitar, Bass, Backing Vocals: Billy Howerdel Piano, Strings: Paz Lenchantin Drums: Josh Freese | Original: John Lennon Rearrangement: Maynard James Keenan | Emotive | 2004 | |
| "Judith" | Vocals: Maynard James Keenan Guitar, Bass, Backing Vocals: Billy Howerdel Backing Vocals: Paz Lenchantin Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Mer de Noms | 2000 | |
| "Kindred" | Vocals: Maynard James Keenan Guitar, Bass, Backing Vocals: Billy Howerdel Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Sessanta E.P.P.P. | 2024 | |
"Let's Have a War"
| Vocals: Maynard James Keenan Guitar, Bass: Danny Lohner Drums: Josh Freese | Original: Lee Ving, Philo Cramer Rearrangement: Maynard James Keenan | Emotive | 2004 | |
| "Lullaby" | Vocals: Jarboe, Maynard James Keenan Guitar: Billy Howerdel Bass: Jeordie White Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Thirteenth Step | 2003 | |
| "Magdalena" | Vocals: Maynard James Keenan Guitar, Bass: Billy Howerdel Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Mer de Noms | 2000 | |
| "The Noose" | Vocals: Maynard James Keenan Backing Vocals: Jarboe Guitar, Backing Vocals: Billy Howerdel Guitar: Danny Lohner Bass: Jeordie White Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Thirteenth Step | 2003 | |
"The Nurse Who Loved Me"
| Vocals: Maynard James Keenan Strings: The Section Quartet | Greg Edwards, Ken Andrews Instrumentation: Jon Brion, [|K]. Patrick Warren | Thirteenth Step | 2003 | |
| "Orestes" | Vocals: Maynard James Keenan Guitar, Bass, Keyboards, Backing Vocals: Billy Howerdel Backing Vocals: Paz Lenchantin Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Mer de Noms | 2000 | |
| "Orestes" | Vocals, Guitar: Billy Howerdel | Billy Howerdel | Mer de Noms | 2000 | |
| "The Outsider" | Vocals: Maynard James Keenan Guitar, Backing Vocals: Billy Howerdel Bass: Jeordie White Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Thirteenth Step | 2003 | |
| "Over" | Vocals, Kalimba: Maynard James Keenan Piano: Billy Howerdel | Maynard James Keenan Billy Howerdel | Mer de Noms | 2000 | |
| "The Package" | Vocals: Maynard James Keenan Guitar, Backing Vocals: Billy Howerdel Guitar: Troy Van Leeuwen Bass: Jeordie White Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Thirteenth Step | 2003 | |
"Passive" | Vocals: Maynard James Keenan Guitar, Backing Vocals: Billy Howerdel Guitar, Bass: Danny Lohner Drums: Josh Freese Piano: Paz Lenchantin | Danny Lohner, Maynard James Keenan, Trent Reznor, Billy Howerdel | Emotive | 2004 | |
"Peace, Love, and Understanding"
| Vocals, Guitar, Bass, Programming: Billy Howerdel Strings: Paz Lenchantin Drums: Josh Freese Programming: Charlie Clouser | Original: Nick Lowe Rearrangement: Billy Howerdel | Emotive | 2004 | |
"People Are People" | Vocals, Keyboards, Programming: Billy Howerdel Backing vocals: Maynard James Keenan, Danny Lohner Guitar, Keyboards, Programming: James Iha Bass: Jeordie White Drums: Josh Freese | Original: Martin Gore Rearrangement: Billy Howerdel | Emotive | 2004 | |
| "Pet" | Vocals: Maynard James Keenan Backing Vocals: Devo Keenan Guitar, Backing Vocals: Billy Howerdel Bass, Backing Vocals: Jeordie White Drums, Backing Vocals: Josh Freese | Maynard James Keenan Billy Howerdel | Thirteenth Step | 2003 | |
| "Renholdër" | Vocals: Maynard James Keenan Vocals: Kelli Shafer Vocals, Guitar, Piano: Billy Howerdel Vocals, Violin: Paz Lenchantin Drums, Percussion: Josh Freese | Maynard James Keenan Billy Howerdel | Mer de Noms | 2000 | |
| "Rose" | Vocals: Maynard James Keenan Guitar, Bass: Billy Howerdel Violin: Paz Lenchantin Drums: Josh Freese | Maynard James Keenan Billy Howerdel Strings Arrangement: Paz Lenchantin | Mer de Noms | 2000 | |
| "Sleeping Beauty" | Vocals: Maynard James Keenan Guitar: Billy Howerdel Guitar : Troy Van Leeuwen Bass: Paz Lenchantin Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Mer de Noms | 2000 | |
| "So Long, and Thanks for All the Fish" | Vocals: Maynard James Keenan Guitar, Bass, Keyboard: Billy Howerdel Drums: Jeff Friedl Strings Arrangement: Dave Sardy | Maynard James Keenan Billy Howerdel | Eat the Elephant | 2018 | |
| "TalkTalk" | Vocals: Maynard James Keenan Guitar, Bass, Keyboard: Billy Howerdel Drums: Jeff Friedl | Maynard James Keenan Billy Howerdel | Eat the Elephant | 2018 | |
| "Thomas" | Vocals: Maynard James Keenan Guitar, Bass, Programming: Billy Howerdel Drums: Josh Freese Percussion: Draven Godwin | Maynard James Keenan Billy Howerdel | Mer de Noms | 2000 | |
| "Thinking of You" | Vocals: Maynard James Keenan Backing Vocals, Guitar, Bass, Programming: Billy Howerdel Guitar : Troy Van Leeuwen Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Mer de Noms | 2000 | |
| "Vanishing" | Vocals: Maynard James Keenan Guitar, Backing Vocals: Billy Howerdel Guitar: Troy Van Leeuwen Bass: Jeordie White Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Thirteenth Step | 2003 | |
| "Weak and Powerless" | Vocals: Maynard James Keenan Guitar, Backing Vocals: Billy Howerdel Bass: Jeordie White Drums: Josh Freese | Maynard James Keenan Billy Howerdel | Thirteenth Step | 2003 | |
"What's Going On" | Vocals: Maynard James Keenan Vocals, Guitar, Bass: Billy Howerdel Drums: Josh Freese Programming: Charlie Clouser | Original: Marvin Gaye, Alfred Cleveland, Renaldo Benson Rearrangement: Danny Lohner | Emotive | 2004 | |
"When the Levee Breaks"
| Vocals: Maynard James Keenan Guitar, Bass: Billy Howerdel Piano: Paz Lenchantin Drums: Josh Freese | Original: Kansas Joe McCoy & Memphis Minnie Rearrangement: Maynard James Keenan, Billy Howerdel | Emotive | 2004 | |