- Ep: 1
- Escape to Beer Mountain: A Rope of Sand
- Special Guest Star: Michael J. Fox (Gandhi's Remaining Kidney)
- Also Starring: Andy Dick (Mr. Sheepman / Vincent Van Gogh / Cop), Donald Faison (George Washington Carver / Wally), Neil Flynn (Carl)
- Uncredited: Bill Lawrence (The Shadowy Figure)
- Featuring Music By: Abandoned Pools, Balloon Records, Bumblefoot, Dashboard Confessional, The Get Up Kids, The Mink Lungs, Ritalin
- Written By: Phil Lord & Christopher Miller & Bill Lawrence
- Ep: 2
- Election Blu Galoo
- Special Guest Star: Marilyn Manson (Himself)
- Also Starring: Donald Faison (X-Stream Bob / Wally), Neil Flynn ( ), Zach Braff (X-Stream Mike), Sarah Chalke (X-Stream Erin)
- Uncredited: Bill Lawrence (The Shadowy Figure)
- Featuring Music By: Jo Davidson, Ephemera, Abandoned Pools, Margo Guryan, Mother West, Vagrant Records, Side One Dummy Records
- Written By: Phil Lord & Christopher Miller
- Ep: 3
- ADD: The Last D is For Disorder
- Special Guest Star: Tom Green (Himself)
- Also Starring: Andy Dick (Mr. Sheepman), Donald Faison (Toots / Wally), Neil Flynn (Julius Caesar / Carl), Zach Braff (Paul Revere), Jeff Garcia (Jesús Cristo)
- Featuring Music By: Saves the Day, The Stereo, Mother West, Jon Derosa, Big Sur, Ephemera
- Written By: Tom Martin
- Ep: 4
- Film Fest: Tears of a Clone
- Also Starring: Andy Dick (Mr. Sheepman / Thomas Edison / Cop), Donald Faison (George Washington Carver), Neil Flynn (Julius Caesar)
- Uncredited: Bill Lawrence (The Shadowy Figure)
- Featuring Music By: The Stereo, Illyah Kuyahkin, Big Sur, Balloon Records, Jon Derosa, Sundays Best, Ritalin
- Written By: Erica Rivinoja
- Ep: 5
- Sleep of Faith: La Rue D'Awakening
- Also Starring: Donald Faison (George Washington Carver), Neil Flynn (Gandhi's Foster Father / Zoo Worker), Judah Miller (Scangrade), John C. McGinley (Creepy Trucker)
- Uncredited: Bill Lawrence (The Shadowy Figure)
- Featuring Music By: The Tremors, Hot Rod Circuit, Lazy Bones, Kill Your Idols, Snap Case, Thursday, Owen
- Written By: Judah Miller & Murray Miller
- Ep: 6
- Homecoming: A Shot in the D'Arc
- Special Guest Stars: Chris Berman (Himself), Dan Patrick (Himself)
- Also Starring: Donald Faison (Toots / Wally), Neil Flynn (Julius Caesar / Carl)
- Featuring Music By: The Stereo, Cadillac Blind Side, Charles Newman, The Mink Lungs, Snap Case, Jo Davidson, Alkaline Trio, Owen
- Written By: Eric Kentoff
- Ep: 7
- Plane Crazy: Gate Expectations
- Special Guest Star: Ashley Parker Angel (Himself)
- Also Starring: Neil Flynn (Buddy Holly), Debra Wilson (Reporter)
- Featuring Music By: The Impossibles, Cadillac Blind Side, Bumblefoot, Speed Dial, The Gloria Record, Jo Davidson, Lazy Bones Music, Fueled By Raman Records
- Written By: Tom Martin
- Ep: 8
- A Room of One's Clone: The Pie of the Storm
- Also Starring: Andy Dick (Mr. Sheepman), Donald Faison (Martin Luther King Jr. / Toots), Neil Flynn (E-CyboPooch / Moses / Pirate / Rich Man), Sarah Chalke (Cleo's Drunk Foster Mom / Marie Antoinette)
- Uncredited: Bill Lawrence (The Shadowy Figure)
- Featuring Music By: Richard Cheese, Bumblefoot, Sunday's Best, Coufax, Vagrant Records, Lazy Bones Recordings, Birdwatcher
- Written By: Adam Pava
- Ep: 9
- Raisin' the Stakes: A Rock Opera in Three Acts
- Special Guest Star: Jack Black (Pusher / Larry Hardcore)
- Also Starring: Donald Faison (Jimi Hendrix / Wally), Neil Flynn (Julius Caesar), Murray Miller (Catherine the Great)
- Featuring Music By: The Mooney Suzuki, Jon Derosa, Margo Guryan, The Mink Lungs, Spirit Music Group, Arena Rock Recording Company, Elf Power
- Written By: Phil Lord & Christopher Miller
- Ep: 10
- Litter Kills: Literally
- Special Guest Star: Luke Perry (Ponce de Leon)
- Also Starring: Andy Dick (Cop), Donald Falson (George Washington Carver), Neil Flynn (Julius Caesar / Glen the Janitor), Judah Miller (Inmate), Murray Miller (Catherine the Great), Don Novello (Inmate)
- Featuring Music By: Owen, Polyvinyl Records, Big Sur, Whippersnapper, Lazy Bones Music, Jon Derosa, Mother West Records
- Written By: Judah Miller & Murray Miller
- Ep: 11
- Snowflake Day: A Very Special Clone High Holiday Special
- Special Guest Star: Mandy Moore (Herself)
- Also Starring: Donald Faison (Toots / King Kwanzaa / Wally / Guy in Commercial), Neil Flynn (Snowflake Jake / Julius Caesar / Carl), Judah Miller (Dreidelstein), Murray Miller (Catherine the Great), Debra Wilson (Girl in Commercial)
- Featuring Music By: James Stewart, Owen, Qball
- Written By: Erica Rivinoja
- Ep: 12
- Makeover, Makeover, Makeover: The Makeover Episode (part 1)
- Also Starring: Donald Faison (Toots), Neil Flynn ( ), Murray Miller (Catherine the Great), Debra Wilson (Harriet Tubman / Eva Peron), Sarah Chalke (Marie Antoinette)
- Uncredited: Bill Lawrence (The Shadowy Figure)
- Featuring Music By: Richard Cheese, Lazy Bones Music Library, Balloon Records, Bumblefoot, Vagrant Records, Spirit Music Group
- Written By: Eric Kentoff
- Ep: 13
- Changes: You Got a Prom Wit Dat? (part 2)
- Special Guest Stars: John Stamos (Himself), Tommy Walter (Himself)
- Also Starring: Andy Dick (Mr. Sheepman / Thomas Edison / Sex Education Officer), Donald Faison (Toots), Neil Flynn (Julius Caesar / Moses / Tux Guy), Judah Miller (Scangrade), Joe Flaherty (Abe's Foster Dad)
- Uncredited: Bill Lawrence (The Shadowy Figure)
- Featuring Music By: Polyvinyl Records, Catch 22, Jinnrail, Victory Records, The Stereo, Abandoned Pools, Snapcase, Fueled By Ramen Records
- Written By: Phil Lord & Christopher Miller
| Will Forte .......................... Abe Lincoln / Narrator |
| Phil Lord ... Principal Cinnamon J. Scudworth / Genghis Khan |
| Michael McDonald .................................... Gandhi |
| Christa Miller Lawrence .......................... Cleopatra |
| Christopher R. Miller ................. JFK / Mr. Butlertron |
| Nicole Sullivan .................. Joan of Arc / Marie Curie |
