After a disastrous limited distribution in 1993, the film was recalled and heavily re-edited for a 1994 re-release.
Gus Van Sant's original version was first shown at the Toronto Film Festival in 1993 before the film was pulled at his own request and reworked. The most significant differences are described in a N.Y.Times article from May 15 1994: "The New York scenes, and Sissy's relationship with an urbanized Mohawk Indian (played by Keanu Reeves), were cut back in the interest of beefing up the ranch scenes and focusing more attention on the relationship between Sissy and Bonanza Jellybean, a straight-shooting cowgirl played by Rain Phoenix. The novelist William Burroughs survived the editing. Audiences will see him cross a Manhattan street, look at the traffic and utter three syllables: "Ominous." Roseanne Arnold, however, will see her cameo as a gypsy fortuneteller whittled down to a mini-cameo. Most dramatically, Mr. Van Sant shed an entire subplot, about the mysterious Clock People, keepers of the keys to cosmic consciousness, and the source of the original film's final image (as well as the clock on the paperback cover). In the first version, Sissy became pregnant after making love to the Chink, a loony visionary played by Pat Morita, who tells her she will bear a race of large-thumbed children who will roam the earth in love and peace after surviving an apocalypse. In the final frames of "Cowgirls I," Sissy's child, seen in the womb, makes hitchhiking gestures toward the audience, an invitation to the future." Van Sant is quoted in the article, that he doesn't know which version is better.