| 0 | Batman Secret Files and Origins | cover | 1 | pencils: Scott McDaniel; inks: Karl Story; colors: Patrick Martin | Batman [Bruce Wayne] |
| 1 | Batman Secret Files and Origins | credits, title page | 1 | pencils: Scott McDaniel; inks: Graham Nolan | Batman [Bruce Wayne]; Robin [Tim Drake]; Nightwing [Dick Grayson]; Catwoman [Selina Kyle]; Azrael [Jean Paul Valley] |
| 2 | Contents | table of contents | 1 | letters: typeset | |
| 3 | Gazing Back: The Secret Origin of the Batman | comic story | 22 | script: Devin K. Grayson; pencils: Staz Johnson, James A. Hodgkins; inks: James A. Hodgkins; colors: Gloria Vasquez, Digital Chameleon; letters: Bill Oakley | Batman [Bruce Wayne]; Thomas Wayne (dies); Martha Wayne (dies); Alfred Pennyworth |
| 4 | Who is Bruce Wayne? | text story | 3 | script: Chuck Dixon; letters: Tom McCraw | Bruce Wayne [Batman]; Lucius Fox |
| 5 | The Dark Knight Detective | character profile | 2 | script: Scott Beatty; pencils: Mark Buckingham; inks: Mark Buckingham; colors: Tom McCraw | Batman [Bruce Wayne] |
| 6 | Aerial Avenger | character profile | 1 | script: Scott Beatty; pencils: Scott McDaniel; inks: Karl Story; colors: Tom McCraw | Nightwing [Dick Grayson] |
| 7 | The Boy Wonder | character profile | 1 | script: Scott Beatty; pencils: Staz Johnson; inks: Stan Woch; colors: Tom McCraw | Robin [Tim Drake] |
| 8 | Gotham City Police Dept.: Jim Gordon | character profile | 1 | script: Scott Beatty; pencils: Lee Weeks; inks: Lee Weeks; colors: Tom McCraw | Commissioner James Gordon |
| 9 | Gotham City Police Dept.: GCPD | character profile | 1 | script: Scott Beatty; pencils: Jim Aparo; inks: Scott McDaniel; colors: Tom McCraw | Lieutenant Sarah Essen-Gordon; Sargeant Harvey Bullock; Detective Mackenzie Bock [Hardback]; Detective Renee Montoya; Lieutenant Stan Kitch; Detective Caz Calluci; Detective Kevin Soong [Survivor]; Billy Pettit |
| 10 | Guided Tour: The Batcave | comic story | 5 | script: Graham Nolan; pencils: Graham Nolan; inks: Bob McLeod; colors: Tom McCraw; letters: Albert DeGuzman | Robin [Tim Drake]; Alfred Pennyworth |
| 11 | Alfred | character profile | 1 | script: Scott Beatty; pencils: Lee Weeks; inks: Lee Weeks; colors: Tom McCraw | Alfred Pennyworth |
| 12 | Interview: Alfred Pennyworth | text story | 2 | script: Doug Moench; pencils: Jim Aparo; inks: Bill Sienkiewicz; colors: Tom McCraw | Alfred Pennyworth |
| 13 | Birds of Prey | character profile | 1 | script: Scott Beatty; pencils: Gary Frank; inks: John Dell; colors: Tom McCraw | Birds of Prey [Black Canary [Dinah Lance]; Oracle [Barbara Gordon]] |
| 14 | The Urban Enforcer | character profile | 1 | script: Scott Beatty; pencils: Brian Apthorp; inks: Wayne Faucher; colors: Tom McCraw | Huntress [Helena Bertinelli] |
| 15 | The Feline Fatale | character profile | 1 | script: Scott Beatty; pencils: Jim Balent; inks: Jim Balent; colors: Tom McCraw | Catwoman [Selina Kyle] |
| 16 | Upon the Shoulders of Giants: The Men Behind Gotham | text story | 4 | script: Scott Beatty | |
| 17 | The Avenging Angel | character profile | 1 | script: Scott Beatty; pencils: Roger Robinson; inks: James Pascoe; colors: Tom McCraw | Azrael [Jean Paul Valley] |
| 18 | Azrael Supporting Cast | character profile | 1 | script: Scott Beatty; pencils: Roger Robinson; inks: James Pascoe; colors: Tom McCraw | Brian Bryan; Sister Lilhy; Nomoz |
| 19 | The Vigilante Vixen | character profile | 1 | script: Scott Beatty; pencils: Stefano Raffaele; inks: Stan Woch; colors: Tom McCraw | Spoiler [Stephanie Brown] |
| 20 | Lost Pages: How Batman Gets His Equipment | comic story | 2 | script: Chuck Dixon; pencils: Jim Aparo; inks: Tom Palmer; colors: Tom McCraw; letters: Albert DeGuzman | Batman [Bruce Wayne]; Robin [Tim Drake]; Lucius Fox |
| 21 | Batman Timeline | text article | 1 | script: Scott Beatty | |
| 22 | From the Desk of Dr. Dennis O'Goodwin | text article | 1 | script: Kelley Puckett | |