- American Elf (limited edition hardcover; published by Top Shelf) (2004)
- American Elf (softcover; published by Top Shelf) (2004)
- American Elf Vol. 2 (softcover; published by Top Shelf) (2007)
- Atlas 1 (backup story; published by Drawn and Quarterly)
- Bizarro Comics (wrote Hawkman story illustrated by Dylan Horrocks; DC Comics)
- Bogus Dead (zombie anthology with two-page story by Jason Cooley and James Kochalka)
- Conversation (with Craig Thompson; published by Top Shelf) (2004)
- Conversation (with Jeffrey Brown; published by Top Shelf) (2005)
- Cute Manifesto, The (2005; published by Alternative Comics)
- Deadbear, Circus Detective (self-published hardcover)
- Fancy Froglin's Sexy Forest (2003; published by Alternative Comics)
- Fantastic Butterflies (2001; published by Alternative Comics and Highwater Books)
- Horrible Truth About Comics, The (2001; published by Alternative Comics)
- James Kochalka Superstar #1-11 (Self-published mini-comics)
- Kissers (1999; published by Highwater Books)
- Little Mister Man #1-3 (Slave Labor Graphics)
- Magic Boy and Girlfriend (1998; published by Top Shelf)
- Magic Boy and the Robot Elf (2003; published by Top Shelf)
- Mermaid (1998; published by Alternative Comics)
- Monica's story (1999; published by Alternative Comics)
- Monkey Vs. Robot (Vol 1) (First Edition) (2000; published by Top Shelf)
- Monkey Vs. Robot (Vol 1) (Second Edition, smaller size) (2005; published by Top Shelf)
- Monkey vs. Robot (Vol 2): Crystal of Power (2003; published by Top Shelf)
- Noisy Outlaws, Unfriendly Blobs, and Some Other Things (anthology featuring 12-page Kochalka story; 2005; published by McSweeney's)
- Paradise Sucks (Black Eye Books)
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- Peanutbutter & Jeremy #1-4 (2000–2003; published by Alternative Comics)
- Peanutbutter & Jeremy's Best Book Ever (2004; published by Alternative Comics)
- Perfect Planet and Other Stories, The (1999; published by Top Shelf)
- Pinky & Stinky (2002; published by Top Shelf)
- Quit Your Job (1998; published by Alternative Comics)
- Reinventing Everything #1 (self-published mini-comic)
- Reinventing Everything #2 (self-published mini-comic)
- Sketchbook Diaries (Vol 1) (2003; published by Top Shelf)
- Sketchbook Diaries (Vol 2) (2003; published by Top Shelf)
- Sketchbook Diaries (Vol 3) (2003; published by Top Shelf)
- Sketchbook Diaries (Vol 4) (2004; published by Top Shelf)
- Squirrelly Gray (2007; published by Random House)
- Sunburn (2000; published by Alternative Comics)
- Sunturd (2003) (mini-comic written by Jason Cooley, same art as Sunburn)
- SuperF*ckers #1 (2005; published by Top Shelf)
- SuperF*ckers #2 (2005; published by Top Shelf)
- SuperF*ckers #3 (2006; published by Top Shelf)
- SuperF*ckers #4 (2007; published by Top Shelf)
- Tiny Bubbles (1998; published by Highwater Books)
- Top Shelf #1 (anthology title with Kochalka contribution; published by Top Shelf)
- Top Shelf #5 (anthology title with Kochalka contribution; published by Top Shelf)
- Top Shelf #6 (anthology title with Kochalka contribution; published by Top Shelf)
- Top Shelf Asks the Big Questions (anthology title with Kochalka contribution; published by Top Shelf)
- Triple Dare #1-2 (1998–2000; Published by Alternative Comics)
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