Two stars of the movie died at an early age: Jeremy Applegate (Peter Dawson, whose character prays he will never commit suicide) committed suicide with a shotgun on March 23, 2000, and Kim Walker (Heather Chandler, who had the line "Did you have a brain tumor for breakfast?") died of a brain tumor on March 6, 2001.
The role of Heather McNamara, the cheerleader, was originally offered to 17 year old actress Heather Graham. Heather's parents decided against letting her do the role because of the dark subject matter.
Originally, the book that suicidal students supposedly underline "meaningful" passages from was "The Catcher in the Rye". The producers could not get clearance to use this book and it was changed to "Moby Dick" instead.
After they kill Kurt and Ram, Christian Slater's character, J.D., says that, "Football season is over." Rolling Stone magazine published an article with Hunter S. Thompson's suicide note, its title was, "Football Season is Over."
Lying on top of the glass table through which Heather Chandler fell were a copy of the Cliff's Notes for "The Bell Jar" (which was written by Sylvia Plath, who committed suicide) and a magazine with a cover story "The Fall of the American Teenager."
Mid-1990's-era ska/punk band Edna's Goldfish named their song "Veronica Sawyer" after the main character in Heathers. The song's theme of alienation among suburban teenagers reflects the themes of the movie. Reel Big Fish covered the song on their 2009 album "Fame, Fortune and Fornication."
The radio call-in show "Hot Probs" featured in the movie is a version of the now nationally famous KROQ radio show "Loveline", and the radio DJ in the movie is James 'Poorman' Trenton, the creator and original host of "Loveline".
In addition to Westburg High being named after The Replacements frontman Paul Westerberg, another reference to the band occurs later in the film when J.D. says "Color me impressed", which is the title of a song from their album 'Hootenanny'.
The original screenplay had a different ending in which Veronica kills J.D. by shooting him and then straps the bomb (a much larger and more complicated piece of equipment, described as being "a cylinder as large as a television set") to herself, blowing up as J.D. does in the final ending. What is placed in the final ending as JD's boiler-room speech about "imagine I blew up the school, imagine I blew up all the schools" is contained in a suicide note found in Veronica's locker by Heather McNamara and Betty Finn. The movie ends with an eerie prom sequence set in Heaven, tying into JD's assertion that the only place everyone will truly get along is in Heaven. The prom begins with students dancing within their social cliques, then switching partners in odd pairings like metalheads dancing with Heathers and one of the murdered jocks getting his prom picture taken with a tipped cow; the punch being served is the drain cleaner used in the first murder scene, and "Dumptruck" is singing onstage as the entertainment for the evening. This was intended to be shot but the studio thought it was too dark for the target teenage crowd and opted for a lighter ending.