During the production, MGM opted not to shoot the "nightmare train" sequence to keep costs down. H.R. Giger was not willing to accept that, however, so he spent one hundred thousand dollars of his own money to finance the sequence.
Michael Madsen once claimed this was one of the few movies he had done that he was proud of, but referred to the film's sequel as "lousy" and admitted he only did it for a paycheck.
Frank Welker, who provided Sil's alien sound effects, said it was one of the most strenuous on his vocal chords with the various types of screaming and screeching sounds he was asked to create, but he had a lot of fun regardless.
H.R. Giger had envisioned more stages of Sil's transformation, but the film only employed the last one. Giger also envisioned Sil glowing with red-orange heat, getting brighter and hotter as she got angrier or felt more threatened. The studio claimed such a thing would be impossible, and when Giger had test designs made to show it could be done, they still refused.
Director Roger Donaldson said in an interview for Starlog Magazine in August of 1995 that the first cut of the Editor Conrad Buff IV put together was two hours and seven minutes long, and it had a different ending action sequence and battle with Sil. A few shots from the original ending can be seen in the theatrical trailer.
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