Novels
- Strangewood (Signet, 1999)
- Straight On 'Til Morning (Signet, 2001)
- The Ferryman (Signet, 2002)
- The Boys Are Back in Town (Bantam, 2004)
- Wildwood Road (Bantam, 2005)
- Bloodstained Oz - co-authored with James A. Moore (Earthling Publications 2006)
- Baltimore, or The Steadfast Tin Soldier and the Vampire (co-authored with Mike Mignola)
- Poison Ink (Delacorte, 2008)
- Soulless (MTV Books, 2008)
- When Rose Wakes (2010)
- Bloodstained Wonderland - co-authored with James A. Moore (Earthling Publications tbd)
- Fresh Kill - co-authored with James A. Moore (tbd)
The Hidden Cities
The Hidden Cities series all co-authored with Tim Lebbon
- Mind the Gap (Spectra, 2008)
- Map of Moments (Spectra, 2009)
- The Chamber of Ten (Spectra, 2010)
- The Shadow Men (Spectra, 2011)
The Veil
- The Myth Hunters (Bantam, 2006)
- The Borderkind (Bantam, 2007)
- The Lost Ones (Bantam, 2008)
The Shadow Saga
- Of Saints and Shadows (Berkley, 1994)
- Angel Souls and Devil Hearts (Berkley, 1995)
- Of Masques and Martyrs (Ace, 1998)
- The Gathering Dark (Berkley, 2003)
- Waking Nightmares (Berkley, 2011)
The Menagerie
The Menagerie series all co-authored with Tom Sniegoski
- The Nimble Man (Ace, 2004)
- Tears of the Furies (Ace, 2005)
- Stones Unturned (Ace, 2006)
- Crashing Paradise (Ace, 2007)
Ghosts of Albion
Ghosts of Albion related books are co-authored with Amber Benson.
- Accursed (Del Rey, 2005)
- Astray (Subterranean, 2005)
- Initiation (Subterranean, 2006)
- Witchery (Del Rey, 2006)
Hellboy
Hellboy related books with cover and other illustrations by Mike Mignola
- Hellboy: The Lost Army (Dark Horse, 1997)
- Hellboy: The Bones of Giants (Dark Horse, 2001)
- Hellboy: The Dragon Pool (Pocket Books, 2007)
Body of Evidence
- Body Bags (Pocket, 1999)
- Thief of Hearts (Pocket, 1999)
- Soul Survivor (Pocket, 1999)
- Meets the Eye (Pocket, 2000)
- Head Games (Pocket, 2000)
- Skin Deep - co-authoered with Rick Hautala (Pocket, 2000)
- Burning Bones - co-authoered with Rick Hautala (Pocket, 2001)
- Brain Trust - co-authoered with Rick Hautala (Pocket, 2001)
- Last Breath - co-authoered with Rick Hautala (Pocket, 2004)
- Throat Culture - co-authoered with Rick Hautala (Pocket, 2005)
OutCast
All co-authored with Tom Sniegoski
- OutCast: The Un-Magician (Pocket, 2004)
- OutCast: Dragon Secrets (Pocket, 2004)
- OutCast: Ghostfire (Pocket, 2005)
- OutCast: Wurm War (Pocket, 2005)
Prowlers
- Prowlers (Pocket, 2001)
- Laws of Nature (Pocket, 2001)
- Predator and Prey (Pocket, 2001)
- Wild Things (Pocket, 2002)
Buffy the Vampire Slayer
Buffy the Vampire Slayer related books.
- Halloween Rain - Co-authored with Nancy Holder (Pocket, 1997)
- Blooded - Co-authored with Nancy Holder (Pocket 1998)
- Child of the Hunt - Co-authored with Nancy Holder (Pocket 1998)
- The Gatekeeper series - all co-authored with Nancy Holder
- Out of the Madhouse (Pocket 1999)
- Ghost Roads (Pocket 1999)
- Sons of Entropy (Pocket 1999)
- Immortal - co-authored with Nancy Holder (hardcover, Pocket, 1999)
- Sins of the Father (Pocket, 1999)
- Pretty Maids All in a Row (hardcover, Pocket, 2000)
- The Lost Slayer a 4 part series(Pocket 2001)
- Prophecies
- Dark Times
- King of the Dead
- Original Sins
- Into the Wild (Pocket, 2002)
- The Wisdom of War (Pocket, 2002)
- Monster Island co-authored with Tom Sniegoski (hardcover, Pocket, 2003)
- Dark Congress (Simon Spotlight, 2007)
Young Adult Novels
- Beach Blanket Psycho (Bantam YA, 1995)
- Bikini (Bantam YA, 1995)
- Force Majeure co-authored with Tom Sniegoski (Pocket, 2002)
- Poison Ink
The Hollow series
Young Adult series co-authored with Ford Lytle Gilmore. The series is based on Washington Irving's
The Legend of Sleepy Hollow.
- Horseman (Pocket, 2005)
- Drowned (Pocket, 2005)
- Mischief (Pocket, 2006)
- Enemies (Pocket, 2006)
The Waking
Young Adult series written under the pseudonym "Thomas Randall"
- Dreams of the Dead (Bloomsbury, 2009)
- Spirits of the Noh (Bloomsbury, 2011)
- A Winter of Ghosts (Bloomsbury, 2011)
The Secret Journeys of Jack London
Young Adult series co-authored with "Tim Lebbon"
- The Wild (HarperCollins, 2011)
- The Sea Wolves (HarperCollins, tbd)
Other Media Tie-ins
Battlestar Galactica
- * Battlestar Galactica: Armageddon
- * Battlestar Galactica: Warhawk
Daredevil
- * Daredevil: Predator's Smile
Genął
- * Genął: Netherwar - co-authored with Jeff Mariotte
Justice League
- * Justice League: Exterminators
King Kong
- * King Kong - official novelization of the 2005 film
X-Men
- * X-Men: Mutant Empire-Siege
- * X-Men: Mutant Empire-Sanctuary
- * X-Men: Mutant Empire-Salvation
- * X-Men: Codename Wolverine
Comics
- Talent (with Thomas E. Sniegoski, Boom! Studios, 2006)
- The Sisterhood (withTom Sniegoski, Archaia, 2008)
- The Plague Ships (with Mike Mignola, Dark Horse Comics, 2010)