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Wagner was born in Madison, Wisconsin, to Morton Wagner and Bernice Maletz. At the age of four, his family moved to San Francisco, then to Los Angeles four years later. He attended Beverly Vista Elementary School in Beverly Hills, CA, until the 8th grade. He attended Beverly Hills High School but dropped out in his junior year. He worked in bookstores, drove an ambulance for Schaefer Ambulance Service, and drove a limousine at the Beverly Hills Hotel.
In his twenties, Wagner began writing articles for magazines, and writing scripts. His first screenplay, Young Lust, was produced by Robert Stigwood but was never released. It was that experience that ultimately led him to write his modern take on F. Scott Fitzgerald's "Pat Hobby" short stories (about an alcoholic screenwriter who never gets ahead).
Wagner self-published (with Caldecott Chubb) Force Majeure: The Bud Wiggins Stories in an edition of 1,000, which sold out at West Hollywood's famed Book Soup. The book was well reviewed and led to a publishing deal with Random House. He is currently published by Blue Rider Press, an imprint at Penguin Books.
He has written essays and op-ed pieces for The New Yorker, The New York Times, Art Forum and Vanity Fair. His novel Still Holding was a New York Times Notable Book of the Year, and his novel The Chrysanthemum Palace was a PEN/Faulkner finalist in 2006. He has also written essays and prefaces for books by photographers William Eggleston and Manuel Alvarez Bravo, painters Ed Ruscha and Richard Prince.
Wagner and Oliver Stone co-executive produced Wild Palms, the mini-series Wagner created, based on a comic strip that he wrote for Details magazine. Wild Palms aired on ABC in 1993. He was the executive producer and co-writer (with Ullman) of Tracey Ullman's State of the Union series on Showtime.
After interviewing Carlos Castaneda for Details magazine in 1994, Wagner became part of Castaneda's inner circle under the assumed name of Lorenzo Drake. He directed the first videos on Tensegrity for Cleargreen and married the mystic Carol Tiggs in 1995. Wagner continues to be close to the group since Castaneda's death in 1998. His first autobiographical piece about his experience with the shaman and author Castaneda appeared in the Fall 2007 issue of Tricycle magazine. After Wagner's novel Memorial was favorably reviewed in that magazine by a Buddhist monk, Wagner wrote its editor, James Shaheen, a letter of thanks, and Shaheen invited him to contribute an essay about Castaneda. More recently, Wagner studied with Indian guru Ramesh Balsekar.
- Force Majeure (1991)
- Wild Palms (1993) (graphic novel)
- I'm Losing You (1996)
- I'll Let You Go (2002)
- Still Holding (2003)
- The Chrysanthemum Palace (2005)
- Memorial (2006)
- Dead Stars (2012)
- The Empty Chair (2014)
- A Nightmare on Elm Street 3: Dream Warriors (1987), "story by" credit, shared with Wes Craven
- Scenes from the Class Struggle in Beverly Hills (1989)
- Wild Palms (1993)
- White Dwarf (1995)
- I'm Losing You (1998), also director
- Women in Film (2001), also director
- Maps to the Stars (2014)