| 0 | Plague of Frogs | cover | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | Abe Sapien |
| 1 | Inside cover blurb | text article | 1 | letters: typeset | |
| 2 | Cast of characters | character profile | 1 | pencils: Guy Davis; inks: Guy Davis | Abe Sapien; Roger; Liz Sherman; Johann Kraus; Kate Corrigan |
| 3 | - | credits, title page | 2 | letters: typeset | |
| 4 | Introduction | foreword, introduction, preface, afterword | 1 | script: Scott Allie | |
| 5 | Book One Hollow Earth and Other Stories | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | Abe Sapien; Roger the Homunculus; Johann Kraus |
| 6 | Hollow Earth | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | Abe Sapien; Roger the Homunculus; Johann Kraus |
| 7 | - | credits, title page | 1 | letters: typeset | |
| 8 | Hollow Earth | comic story | 22 | script: Mike Mignola, Christopher Golden, Tom Sniegoski; pencils: Ryan Sook; inks: Ryan Sook; colors: Dave Stewart; letters: Clem Robins | Liz Sherman; Kate Corrigan; Johann Kraus (see notes); Hellboy (flashback only); Tom Manning; Abe Sapien; Roger the Homunculus; other B.P.R.D. operatives |
| 9 | Hollow Earth | comic story | 22 | script: Mike Mignola, Christopher Golden, Tom Sniegoski; pencils: Ryan Sook; inks: Ryan Sook, Curtis Arnold; colors: Dave Stewart; letters: Clem Robins | Abe Sapien; Liz Sherman; Roger the Homunculus; Kate Corrigan; Johann Kraus; Hellboy (flashback only); Trevor Bruttenholm (flashback only); other B.P.R.D. operatives; the King of Fear (first appearance; cameo) |
| 10 | Hollow Earth | comic story | 22 | script: Mike Mignola, Christopher Golden, Tom Sniegoski; pencils: Ryan Sook; inks: Curtis Arnold; colors: Dave Stewart; letters: Clem Robins | Liz Sherman; Hellboy (flashback only); Roger the Homunculus; Abe Sapien; Johann Kraus; the King of Fear; Kate Corrigan; other B.P.R.D. operatives |
| 11 | - | credits, title page | 1 | letters: typeset | |
| 12 | Hollow Earth [Prologue] | comic story | 1 | script: Mike Mignola, Christopher Golden, Tom Sniegoski; pencils: Ryan Sook; inks: Ryan Sook; colors: Dave Stewart; letters: Dan Jackson | Kate Corrigan; Johann Kraus (origin, introduction) |
| 13 | Hollow Earth | comic story | 1 | script: Mike Mignola, Christopher Golden, Tom Sniegoski; pencils: Ryan Sook; inks: Ryan Sook, Curtis Arnold; colors: Dave Stewart; letters: Dan Jackson | B.P.R.D. [Kate Corrigan]; Johann Kraus |
| 14 | Hollow Earth | comic story | 1 | script: Mike Mignola, Christopher Golden, Tom Sniegoski; pencils: Ryan Sook; inks: Ryan Sook; colors: Dave Stewart; letters: Dan Jackson | Kate Corrigan; Johann Kraus (origin) |
| 15 | The Killer in My Skull & Abe Sapien Versus Science | illustration | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | Abe Sapien |
| 16 | - | credits, title page | 1 | letters: typeset | |
| 17 | The Killer in My Skull | comic story | 10 | script: Mike Mignola; pencils: Matt Smith; inks: Ryan Sook; colors: Dave Stewart; letters: Pat Brosseau | Lobster Johnson [The Lobster] (introduction) |
| 18 | Abe Sapien Versus Science | comic story | 8 | script: Mike Mignola; pencils: Matt Smith; inks: Mike Mignola; colors: Dave Stewart; letters: Pat Brosseau | |
| 19 | Drums of the Dead | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | Abe Sapien; Hellboy (inset) |
| 20 | - | credits, title page | 1 | letters: typeset | |
| 21 | Drums of the Dead | comic story | 22 | script: Brian McDonald; pencils: Derek Thompson; inks: Derek Thompson; colors: James Sinclair; letters: Pat Brosseau | Abe Sapien; Tom Manning; Garrett Omatta (introduction) |
| 22 | Book Two The Soul of Venice and Other Stories | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | Johann Kraus; Liz Sherman; Abe Sapien; Roger |
| 23 | The Soul of Venice | cover reprint (on interior page) | 1 | pencils: Michael Avon Oeming; inks: Michael Avon Oeming; colors: Matt Hollingsworth | |
| 24 | - | credits, title page | 1 | letters: typeset | |
| 25 | The Soul Of Venice | comic story | 25 | script: Michael Avon Oeming, Mike Mignola, Miles Gunter; pencils: Michael Avon Oeming; inks: Michael Avon Oeming; colors: Dave Stewart; letters: Ken Bruzenak | |
| 26 | - | illustration | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | Abe Sapien |
| 27 | Dark Waters | cover reprint (on interior page) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | |
| 28 | - | credits, title page | 1 | letters: typeset | |
| 29 | Dark Waters | comic story | 22 | script: Brian Augustyn; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Michelle Madsen | Abe Sapien; Constable Annie Rachham; Reverend Lucas Shaw; Pastor Blackwood |
| 30 | Night Train | cover reprint (on interior page) | 1 | pencils: Scott Kolins; inks: Scott Kolins; colors: Dave Stewart | |
| 31 | - | credits, title page | 1 | letters: typeset | |
| 32 | Night Train | comic story | 22 | script: Geoff Johns, Scott Kolins; pencils: Scott Kolins; inks: Scott Kolins; colors: Dave Stewart; letters: Pat Brosseau | |
| 33 | There's Something Under My Bed | cover reprint (on interior page) | 1 | pencils: Adam Pollina; inks: Adam Pollina; colors: Dave Stewart | Abe Sapien |
| 34 | - | credits, title page | 1 | letters: typeset | |
| 35 | There's Something Under My Bed | comic story | 22 | script: Joe Harris; pencils: Adam Pollina; inks: Guillermo Zubiaga; colors: Lee Loughridge; letters: Pat Brosseau | Abe Sapien; Johann Kraus; Liz Sherman |
| 36 | Another Day at the Office | comic story | 8 | script: Mike Mignola; pencils: Cameron Stewart; inks: Cameron Stewart; colors: Dave Stewart; letters: Michael Heisler | B.P.R.D. [Abe Sapien; Johann Kraus; Rachel Turner]; Robert Huntley; Yegor Kurya |
| 37 | Plague of Frogs | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | Liz Sherman; Abe Sapien; Johann Kraus; Roger |
| 38 | - | credits, title page | 1 | letters: typeset | |
| 39 | Chapter One | cover reprint (on interior page) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | Abe Sapien; Johann Kraus; Liz Sherman; Roger the Homunculus |
| 40 | Plague of Frogs | comic story | 24 | script: Mike Mignola; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Abe Sapien; Dr. Kate Corrigan; Liz Sherman; Roger; Johann Kraus |
| 41 | Chapter Two | cover reprint (on interior page) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | Roger the Homunculus |
| 42 | Plague of Frogs | comic story | 24 | script: Mike Mignola; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Abe Sapien; Dr. Kate Corrigan; Liz Sherman; Roger; Johann Kraus |
| 43 | Chapter Three | cover reprint (on interior page) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | Abe Sapien; Liz Sherman |
| 44 | Plague of Frogs | comic story | 24 | script: Mike Mignola; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Abe Sapien; Dr. Kate Corrigan; Liz Sherman; Roger; Johann Kraus |
| 45 | Chapter Four | cover reprint (on interior page) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | Liz Sherman |
| 46 | Plague of Frogs | comic story | 24 | script: Mike Mignola; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Abe Sapien; Dr. Kate Corrigan; Liz Sherman; Roger the Homunculus; Johann Kraus |
| 47 | Chapter Five | cover reprint (on interior page) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | Abe Sapien |
| 48 | Plague of Frogs | comic story | 24 | script: Mike Mignola; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Abe Sapien; Dr. Kate Corrigan; Liz Sherman; Roger the Homunculus; Johann Kraus |
| 49 | Afterword | foreword, introduction, preface, afterword | 1 | script: Mike Mignola | |
| 50 | Hollow Earth Sketchbook | illustration | 9 | script: Scott Allie; pencils: Mike Mignola, Ryan Sook; colors: Ryan Sook; letters: Mike Mignola | |
| 51 | The Soul of Venice and Other Stories Sketchbook | illustration | 15 | script: Scott Allie, Scott Kolins, Michael Avon Oeming, Joe Harris, Guy Davis, Cameron Stewart; pencils: Scott Kolins, Michael Avon Oeming, Adam Pollina, Guy Davis, Cameron Stewart; inks: Scott Kolins, Michael Avon Oeming, Cameron Stewart; letters: Guy Davis | |
| 52 | Plague of Frogs Sketchbook | illustration | 13 | script: Scott Allie; pencils: Guy Davis; inks: Guy Davis; letters: Guy Davis | |
| 53 | Recommended Dark Horse Reading | promo (ad from the publisher) | 1 | pencils: various; inks: various; colors: various; letters: typeset | |
| 54 | Hellboy by Mike Mignola | promo (ad from the publisher) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | |
| 55 | Mike Mignola; Guy Davis | text article | 1 | pencils: ? (photograph); inks: ? (photograph); colors: ? (photograph); letters: typeset | Mike Mignola |
| 56 | back cover | promo (ad from the publisher) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | |