Volumes 1-7 are published by Fantagraphics; volumes 8-up are published by Dark Horse Comics. Hardcover versions of the Dark Horse collections often include exclusive extras; some of this material was included in the 2004 artbook, also published by Dark Horse.
- Book 1: The Ronin
- Book 2: Samurai
- Book 3: The Wanderer's Road
- Book 4: The Dragon Bellow Conspiracy
- Book 5: Lone Goat and Kid
- Book 6: Circles
- Book 7: Gen's Story
- Book 8: Shades of Death
- Book 9: Daisho
- Book 10: The Brink of Life and Death
- Book 11: Seasons
- Book 12: Grasscutter
- Book 13: Grey Shadows
- Book 14: Demon Mask
- Book 15: Grasscutter II: Journey to Atsuta Shrine
- Book 16: The Shrouded Moon
- Book 17: Duel at Kitanoji
- Book 18: Travels With Jotaro
- Book 19: Fathers and Sons
- Book 20: Glimpses of Death
- Book 21: The Mother of Mountains
- Book 22: Tomoe's Story
- Book 23: Bridge of Tears
- Book 24: Return of the Black Soul
- Book 25: Fox Hunt
- Book 26: Traitors of the Earth
- Book 27: A Town Called Hell
- Book 28: Red Scorpion
- Book 29: Two Hundred Jizo
- Book 30: Thieves and Spies
- Book 31: The Hell Screen
- Book 32: Mysteries
- Book 33: The Hidden
- Space Usagi
Larger Collections 
Edit
- Usagi Yojimbo: The Special Edition
- The Usagi Yojimbo Saga Volume 1
- The Usagi Yojimbo Saga Volume 2
- The Usagi Yojimbo Saga Volume 3
- The Usagi Yojimbo Saga Volume 4
- The Usagi Yojimbo Saga Volume 5
- The Usagi Yojimbo Saga Volume 6
- The Usagi Yojimbo Saga Volume 7
- The Usagi Yojimbo Saga Volume 8
- The Usagi Yojimbo Saga: Legends
- Usagi Yojimbo Gallery Edition Volume 1: Samurai and Other Stories
- Usagi Yojimbo Gallery Edition Volume 2: The Artist and Other Stories
Other Collections Edit
- The Art of Usagi Yojimbo: 20th Anniversary Edition, published 2004.
- Usagi Yojimbo: Yokai
- The Sakai Project
- Usagi Yojimbo: Senso
- Usagi Yojimbo Dojo 20th Anniversary Special
- Teenage Mutant Ninja Turtles/Usagi Yojimbo
- Usagi Yojimbo/Teenage Mutant Ninja Turtles: The Complete Collection
- The Usagi Yojimbo Sketchbook #1
- The Usagi Yojimbo Sketchbook #2
- The Usagi Yojimbo Sketchbook #3
- The Usagi Yojimbo Sketchbook #4
- The Usagi Yojimbo Sketchbook #5
- The Usagi Yojimbo Sketchbook #6
- The Usagi Yojimbo Sketchbook #7
- The Usagi Yojimbo Sketchbook #8
- The Usagi Yojimbo Sketchbook #9
- The Usagi Yojimbo Sketchbook #10
- The Usagi Yojimbo Sketchbook #11
- The Usagi Yojimbo Sketchbook #12
- The Usagi Yojimbo Sketchbook #13
