| 0 | - | cover | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai | Jotaro, Miyamoto Usagi |
| 1 | Title Page and Credits | credits, title page | 4 | pencils: Stan Sakai; inks: Stan Sakai | |
| 2 | Dedication | foreword, introduction, preface, afterword | 1 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai | |
| 3 | Contents | table of contents | 2 | pencils: Stan Sakai; inks: Stan Sakai | |
| 4 | Cast of Characters | character profile | 1 | pencils: Stan Sakai; inks: Stan Sakai | |
| 5 | A Cartoon Appreciation | cartoon | 1 | script: Jack Davis; pencils: Jack Davis; inks: Jack Davis; letters: Jack Davis | |
| 6 | Vendetta | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 7 | The Return of the Lone Goat and Kid | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 8 | Images from a Winter's Day | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 9 | Koji | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 10 | A Lesson in Courtesy | comic story | 4 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; colors: Jason Hvam; letters: Stan Sakai | Katsuichi, Miyamoto Usagi |
| 11 | Crows Part One | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Katsuichi |
| 12 | Crows Part Two | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Katsuichi, Miyamoto Usagi |
| 13 | Crows Part Three | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Katsuichi, Miyamoto Usagi |
| 14 | Duel at Kitanoji | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Katsuichi, Miyamoto Usagi |
| 15 | Introduction | foreword, introduction, preface, afterword | 2 | script: Peter Laird; pencils: Stan Sakai; inks: Stan Sakai | |
| 16 | Out of the Shadows | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Chizu, Jotaro, Miyamoto Usagi |
| 17 | Ghost Warriors | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Miyamoto Usagi |
| 18 | Komainu | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Kitsune, Miyamoto Usagi |
| 19 | Tamago | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Miyamoto Usagi |
| 20 | Usagi and the Tengu | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Katsuichi, Miyamoto Usagi |
| 21 | Sumi-E Part One | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Miyamoto Usagi, Sasuké |
| 22 | Sumi-E Part Two | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Miyamoto Usagi, Sasuké |
| 23 | Sumi-E Part Three | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Miyamoto Usagi, Sasuké |
| 24 | Introduction | foreword, introduction, preface, afterword | 1 | script: Matt Wagner; pencils: Stan Sakai; inks: Stan Sakai | |
| 25 | Fathers and Sons Part One | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Miyamoto Usagi |
| 26 | Fathers and Sons Part Two | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Miyamoto Usagi |
| 27 | Bells | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Katsuichi |
| 28 | Kill the Geishu Lord! | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Miyamoto Usagi, Tomoe Ame |
| 29 | The Pride of the Samurai | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Miyamoto Usagi, Tomoe Ame |
| 30 | Hokashi, Part 1 | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jotaro, Katsuichi, Miyamoto Usagi |
| 31 | Hokashi Part 2 | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Hannah Sakai; letters: Stan Sakai | Jotaro, Katsuichi, Miyamoto Usagi |
| 32 | Story Notes | text article | 6 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai | |
| 33 | Usagi Yojimbo Volume Three #53 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 34 | Usagi Yojimbo Volume Three #54 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 35 | Usagi Yojimbo Volume Three #55 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 36 | Usagi Yojimbo Volume Three #56 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 37 | Usagi Yojimbo Volume Three #57 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro, Katsuichi |
| 38 | Usagi Yojimbo Volume Three #58 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro, Miyamoto Usagi |
| 39 | Usagi Yojimbo Volume Three #59 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro, Katsuichi, Miyamoto Usagi |
| 40 | Usagi Yojimbo Volume Three #60 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Katsuichi |
| 41 | Usagi Yojimbo Volume Three #61 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro, Miyamoto Usagi |
| 42 | Usagi Yojimbo Volume Three #62 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro, Miyamoto Usagi |
| 43 | Usagi Yojimbo Volume Three #63 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro, Miyamoto Usagi |
| 44 | Usagi Yojimbo Volume Three #64 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro, Miyamoto Usagi |
| 45 | Usagi Yojimbo Volume Three #65 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 46 | Usagi Yojimbo Volume Three #66 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 47 | Usagi Yojimbo Volume Three #67 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro |
| 48 | Usagi Yojimbo Volume Three #68 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 49 | Usagi Yojimbo Volume Three #69 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro |
| 50 | Usagi Yojimbo Volume Three #70 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro, Miyamoto Usagi |
| 51 | Usagi Yojimbo Volume Three #71 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Katsuichi |
| 52 | Usagi Yojimbo Volume Three #72 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro, Miyamoto Usagi, Tomoe Ame |
| 53 | Usagi Yojimbo Volume Three #73 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro, Miyamoto Usagi |
| 54 | Usagi Yojimbo Volume Three #74 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro, Miyamoto Usagi |
| 55 | Usagi Yojimbo Volume Three #75 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jotaro, Miyamoto Usagi |
| 56 | Usagi Yojimbo Book 17: Duel at Kitanoji | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai | Katsuichi, Miyamoto Usagi |
| 57 | Usagi Yojimbo Book 18: Travels with Jotaro | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai | Jotaro, Miyamoto Usagi |
| 58 | Usagi Yojimbo Book 19: Fathers and Sons | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai | Jotaro, Miyamoto Usagi |
| 59 | Sketchbook | illustration | 4 | pencils: Stan Sakai | |
| 60 | Pinups | illustration | 2 | pencils: Andi Watson, Jay Hosler, Jay Stephens, Art Baltazar, Guy Davis; inks: Andi Watson, Jay Hosler, Jay Stephens, Art Baltazar, Guy Davis | Miyamoto Usagi |