Homosexuality is integral to Heim's writing, although in interviews he has stressed that he does not want to be "tagged as a gay writer." "Being gay is not the focal point of what I write," he explained in a 1997 profile. "There's a new attitude among writers where there doesn't have to be an apology for gayness in literature. You used to have to explain what being gay was before you introduced it in your writing. That's not the case anymore, and I hope my writing reflects that. I also hope my audience will let me go on to other things besides my sexuality."

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Although Heim has disavowed the label "gay writer," he has declared that he is "most interested in the psychology behind the darker human impulses: violence, addictive behavior, 'illicit' or 'taboo' sex."

Heim was born on September 26, 1966 in Hutchinson, Kansas, a small farming community. He earned a B.A. in English and Art History from the University of Kansas at Lawrence in 1989 and an M.A. in English Literature in 1991. Two years later he received a Master of Fine Arts Degree from Columbia University in Fiction Writing.

He began writing "horror stories . . . for my friends" when he was ten or eleven years old. Later, in high school he turned to writing confessional, lyrical poetry although his work became "more and more narrative." By the time he entered college his interests had turned to fiction writing. "At that stage," Heim recalled, "the only difference between [my poetry] and my fiction was that the poems were more economical and didn't have to explain things like character and plot." His first published work was the poetry collection Saved from Drowning (1993).

In 1995, Heim published his first novel, Mysterious Skin, which he had begun writing while still a graduate student at Columbia University. The novel, set in small-town Kansas, concerns Brian Lackey, a young man who attempts to fill a blank space in his life as he remembers "The summer I was eight years old, five hours disappeared from my life."

The key to Brian's recovery of those lost hours is Neil McCormick, a fellow former member of the local Little League baseball team, who has grown up to be a teenage gay hustler. While both Brian and Neil had been sexually abused as children by their baseball coach, their reactions to the experience differ widely. Brian blocks the incident from his memory, and instead convinces himself that he had been abducted by aliens during those missing hours, while Neil feels "honored" by the coach's attention.

Heim won near-universal critical praise for his deft and sensitive handling of the complicated characters and delicate subject matter of Mysterious Skin. An article in Kirkus Reviews asked, "After reading Heim's debut, one question remains: How will he top this?" and called the novel "as searing and unforgettable as an electric shock." The San Francisco Chronicle noted that "Heim is breathtakingly unafraid to take chances."

In 2003, the playwright Prince Gomolvilas adapted Mysterious Skin for the stage. The play debuted in May of that year at the New Conservatory Theatre Center in San Francisco. In 2004, Gregg Araki, one of the leading figures of the "New Queer Cinema," wrote and directed a film version of Heim's novel. It starred Brady Corbet as Brian and Joseph Gordon-Levitt as Neil. The film was nominated for a 2006 GLAAD Media Award as Outstanding Film.

Heim published his second novel, In Awe, in 1997. It is a psychological horror story about three outcasts in a small university town in Kansas: Boris, a gay teenager; Sarah, a 32-year old nymphomaniac; and Harriet, an elderly woman and mother of Sarah's best friend, Marshall, a young man who has recently died from complications due to AIDS. The trio bands together against the bigotry of a group of locals that leads to an outburst of violence and murder.