| Year | Title | Director [1] | Album |
|---|
| 1984 | "True Men Don't Kill Coyotes" | Graeme Whifler | The Red Hot Chili Peppers |
| 1986 | "Jungle Man" | Lindy Goetz | Freaky Styley |
| "Catholic School Girls Rule" | Dick Rude |
| 1987 | "Fight Like a Brave" | The Uplift Mofo Party Plan |
| 1988 | "Fire" | Live performance | Mother's Milk |
| 1989 | "Good Time Boys" | Drew Carolan |
| "Higher Ground" | Bill Stobaugh and Drew Carolan |
| "Knock Me Down" | Drew Carolan |
| 1990 | "Taste the Pain" | Tom Stern and Alex Winter |
| "Show Me Your Soul" | Bill Stobaugh | Pretty Woman soundtrack |
| 1991 | "Give It Away" | Stéphane Sednaoui | Blood Sugar Sex Magik |
| 1992 | "Under the Bridge" | Gus Van Sant |
| "Under the Bridge" (Version 2) |
| "Under the Bridge" (Version 3) |
| "Suck My Kiss" | Gavin Bowden |
| "Breaking the Girl" | Stéphane Sednaoui |
| "Behind the Sun" | Charlie Paul | The Uplift Mofo Party Plan |
| 1993 | "If You Have to Ask" | Compilation footage | Blood Sugar Sex Magik |
| "Soul to Squeeze" | Kevin Kerslake | Coneheads: Music from the Motion Picture Soundtrack |
| 1995 | "Warped" | Gavin Bowden | One Hot Minute |
| "My Friends" | Anton Corbijn |
| "My Friends" (Version 2) | Gavin Bowden |
| 1996 | "Aeroplane" |
| "Coffee Shop" |
| "Love Rollercoaster" | Kevin Lofton | Beavis and Butthead Do America Soundtrack |
| 1999 | "Scar Tissue" | Stéphane Sednaoui | Californication |
| "Around the World" |
| 2000 | "Otherside" | Jonathan Dayton and Valerie Faris |
| "Californication" |
| "Road Trippin'" |
| 2002 | "By the Way" | By the Way |
| "By the Way" (Version 2) |
| "The Zephyr Song" |
| 2003 | "Can't Stop" | Mark Romanek |
| "Universally Speaking" | Dick Rude |
| "Fortune Faded" | Laurent Briet | Greatest Hits |
| 2006 | "Dani California" | Tony Kaye | Stadium Arcadium |
| "Tell Me Baby" | Jonathan Dayton and Valerie Faris |
| "Snow ((Hey Oh))" | Nick Wickham |
| 2007 | "Charlie" | Omri Cohen |
| "Desecration Smile" | Gus Van Sant |
| "Desecration Smile" (Version 2) |
| "Hump de Bump" | Chris Rock |
| 2011 | "The Adventures of Rain Dance Maggie" | Marc Klasfeld | I'm with You |
| "The Adventures of Rain Dance Maggie" (Version 2 - unreleased) | Kreayshawn |
| "Monarchy of Roses" | Marc Klasfeld |
| 2012 | "Look Around" | Robert Hales |
| "Brendan's Death Song" (radio edit version) | Marc Klasfeld |
| "Brendan's Death Song" (album version) |
| 2016 | "Dark Necessities" [2] | Olivia Wilde | The Getaway |
| "Go Robot" [3] | Thoranna Sigurdardottir aka Tota Lee |
| "Sick Love" | Beth Jeans Houghton |
| 2017 | "Goodbye Angels" | Thoranna Sigurdardottir aka TOTA |
| 2022 | "Black Summer" | Deborah Chow [4] | Unlimited Love |
| "Poster Child" | Julien & Thami |
| "These Are the Ways" | Malia James |
| "Tippa My Tongue" | Return of the Dream Canteen |
| "The Drummer" | Phillip R Lopez |
