- One scene, where Vincent D'Onofrio hangs on his piercings, masturbating over the dead body of a woman, was not included in the US theatrical or DVD release, but can be seen in the European one. However, the US Blu-ray happens to contain the director's cut of the film, despite not being labelled as such on the packaging and the R-rating listed on the back. The runtime is listed as 109 (the length of the director's cut) which marks the first time the film has been released uncut in the US.
- The DVD release features a few deleted scenes:
- Two scenes featuring the girl in the water tank: one where she beats on the glass in the dark, screaming randomly, and another where the water comes on as she tries to eat, she counts to thirty, and screams when the water doesn't shut off when she reaches thirty (this sceen was, in part, in a version of the trailer)
- A scene where, shortly after arriving at the institute, Peter and his partner talk by a statue (completely improvised, according to the director's commentary)
- A previously unseen session with the child in the desert; the session is interuppted by outside influence, and we see a 'green man' speak for the technicians and place the fabric over Lopez's eyes as she passes out (immediately before the scene where one of the technicians says 'We have a situation')
- An extended and modified version of the conversation between Lopez and D'Onofrio at the bathtub (where Carl is taking apart his first victim)
- A modified version of the initial strike on Carl's house, involving a single FBI agent running across the street, over the fence, and onto Carl's lawn; he sees Carl, unconsious on the floor in his kitchen, via mirror (followed immediately by the initial infiltration)
- An incredibly long and slow pan across the ceiling of Carl's room after the long shot of the schoolyard at the very end of the movie
- The European version of the 'hanging' sequence, complete with Carl finishing the preparation of the body
- The Australian DVD from Roadshow contains the 2-minute extended European version, with Stargher masturbating in suspension over the bleached female victim. This release was granted an R 18+ rating by the OFLC, whereas the shorter theatrical version was rated MA 15+.
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