Alternate versions

The Indian theatrical release was cut by 3 minutes by the Censor Board for an 'A' (adults) rating.

• The word 'Cock' spoken by Stathis in the dialogue "What? His cock?".
• Pick-up girl sitting on a chair, and reduced the love-making between her and Seth.
• The abortion dream sequence from the point where Veronica screams to the point where she is shown waking up. This means the visuals of the bloody maggot baby was removed entirely.
• In the climax: a. Seth crushing Stathis's hand. b. Seth vomiting on Stathis. c. Veronica pulling off Seth's jaw as he transforms.

The 5.1 track misses a few extra music cues present in the original stereo mix: -The synthesizer stinger cue whenever we see the fly picture on Seth's computer screen whenever he tries to figure out what went wrong in the first teleportation -When Veronica visits Seth, the synthesizer stinger cue whenever he yells "Stop!" and we see a further phase of his transformation -An extra synthesizer stinger cue when we see Seth's shadow above Stathis near the end -The whole sequence where Seth is attempting to fuse with Veronica there's a synth rumble underneath the score All of these cues were restored to the stereo track of the Shout! Factory blu-ray.

There is a deleted scene of Brundlefly putting the surviving baboon & a cat in the telepod at the same time. The baboon evolves into a catlike creature. This scene is talked about in a book called "Men Makeup & Monsters" by Anthony Timpone and would be included as a bonus feature on subsequent DVD and Blu-ray releases.

A scene where Veronica interviews Brundle about his teleportation (the interview comes after his superhuman exercise sequence) was filmed, but deleted from the final cut. However, an edited version of this scene appears in form of the first videotape of Brundle in The Fly II (1989).

A lengthy shot of Brundle using a fly tongue to suck from Stathis Borans's severed foot was filmed but deleted from the final cut. A rough form of the scene is featured in the retrospective documentary Fear of the Flesh: The Making of 'The Fly' (2005).