Several scenes on the story boards and in the script did not make the final cut of the film. Some weren't even filmed at all. Some of these scenes included a sexual encounter between Dallas and Ripley, who have their moment spoiled in horror when Kane's corpse, which they ejected hours before, drifts in front of their view and bangs into the window. The other more controversial scene that was not even filmed, but only hinted at, was a 'rape' scene involving Lambert and the Alien. The Alien sliding its tail between Lambert's legs was originally intended to be the start of a bizarre sodomy/rape sequence, but director Ridley Scott thought better of it and decided not to film that scene. The only inclination of the alien sodomizing or raping Lambert left in the film is the fact that her corpse, which we only get a brief glimpse of hanging from the ceiling, is stark naked.

Originally the design for the alien called for it to have pulsing brains in its head (the idea being so we could see the creature 'thinking' while it moved around). The effects department accomplished this by having live maggots placed underneath the transparent dome on the head. Unfortunately the maggots refused to wriggle and move around on command, so the effects dept. doused them with LSD right before the cameras started rolling. Sadly the idea was later scrapped.

When Kane is in the egg pit on the alien ship and shines his light on one of the eggs, the shape we see moving inside is in fact the hands of director Ridley Scott clad in rubber gloves.

Originally, director Ridley Scott wanted "Alien" to have a much darker ending. His intention was to have the alien get back on board the shuttle, rip Ripley's head off and then calmly sit down in her chair and record the final transmission, speaking in her voice. The producers understandably found this a little too extreme, so Scott tried changing it to having Ripley go to sleep as normal only for the camera to pull back out of the airlock's window and reveal an alien egg, in the process of hatching, attached to the outside of the shuttle (after the "Brett/Dallas egg mutation" scene was deleted, this also had to go).

For the wide shots where we see Kane and Co. walking around outside the Nostromo, Ridley Scott used children (two of which were his own) in special child sized space suits so the sets would appear bigger in comparison to the people on screen. He used the same tactic again when they discover the fossilised space jockey on the alien ship.