Novels and novelette

• The Mirror (novella) (1987)
• The Story of a Bad Cat (1987)
• Do You Know Me (1993)
• The Ear, the Eye and the Arm (1994)
• A Girl Named Disaster (1996)
• The Warm Place (1996)
• The House of the Scorpion (2002)

The Sea of Trolls Trilogy

• The Sea of Trolls (2004)
• The Land of the Silver Apples (2007)
• The Islands of the Blessed (2009)

Picture Books

• Runnery Granary: A Mystery Must Be Solved...Or the Grain is Lost!, illustrated by Jos. A. Smith (1996)
• Casey Jones's Fireman: The Story of Sim Webb, illustrated by James Bernardin (1999)
• Clever Ali, illustrated by Gail De Marcken (2006)

Short stories

• “Tapiwa’s Uncle” - in Cricket (February 1992)
• "Origami Mountain" - in The Year's Best Fantasy and Horror: Sixth Annual Collection (1992)
• "Falada: the Goose Girl's Horse" - in A Wolf At the Door, eds. Ellen Datlow and Terri Windling (2000)
• "Remember Me" - in Firebirds: An Anthology of Original Fantasy and Science Fiction, ed. Sharyn November (2003)
• "Bella's Birthday Present" - in Can You Keep a Secret, ed. Lois Metzger (2007)
• "The Mole Cure" - in Fantasy and Science Fiction (August 2007)
• "Ticket to Ride" - in Firebirds Soaring: An Anthology of Original Speculative Fiction, ed. Sharyn November (2008)
• "Castle Othello" - in Troll's Eye View, eds. Ellen Datlow and Terri Windling (2009)

• 1995, Newbery Honor for The Ear, the Eye and the Arm (1994)
• 1996, National Book Award (U.S.) Finalist, Young People's Literature category, for A Girl Named Disaster (1996)
• 1997, Newbery Honor for A Girl Named Disaster (1996)
• 2002, National Book Award (U.S.), Young People's Literature category, for The House of the Scorpion (2002)
• 2003, Newbery Honor for The House of the Scorpion (2002)
• 2003, Buxtehuder Bulle (Germany) for The House of the Scorpion (2002)
• 2003, Printz Honor for The House of the Scorpion (2002)