Alternate versions

USA laserdisc edition adds a few scenes deleted from theatrical release as a bonus at the end of the program, including: a prologue where Somerset (Morgan Freeman) is going to buy a country house. He uses his switchblade (seen many times in the final cut, but not explained) to cut out a small piece of wallpaper. There is an extended scene at the Mills' when David (Brad Pitt) is playing with his dogs, and Somerset talks to Tracy. He tells her about the house and shows her the wallpaper. She tells him that it wouldn't be such a good idea to show it to David, saying "He wouldn't understand.". These two scenes establish Somerset's characters better, and the second one helps the viewer understand why the wife chooses Somerset to talk to when she gets pregnant. She knows that Somerset is much more sensible than her husband, and will understand her. The second one however was probably dumped earlier since it is included among the dailies and outtakes and the first one appears as a deleted scene.

In the US version, Tracy Mills (Gwyneth Paltrow) calls her husband at the office and asks to speak to Detective Somerset (Morgan Freeman). We see them talking on the phone but only hear what Detective Mills (Brad Pitt) and Somerset say. When Somerset hangs up, he explains to Mills that his wife has invited him over for dinner. In the Italian version Tracy's dialogue has been dubbed over the soundtrack, letting the audience hear her talking on the phone and making the invitation, thus rendering Somerset's later explanation somewhat redundant.

In the Platinum Series DVD released by New Line on 12/19/2000, Mills has a line just as Somerset runs up to him in the climactic scene. The line is supposed to be "What the f***'s he talking about?" Clearly audible on the Criterion laserdisc, this line is obscured on the new DVD because the director, while remastering the sound for the new release, thought that the character should be whispering the line to himself rather than yelling it, as it was on the Criterion laserdisc. Thus, it was altered. The song used for the opening credit sequence is a remix of a remix of "Closer" by Nine Inch Nails. It was credited as "Closer (Precursor) (Remix)" by Nine Inch Nails on the Criterion laserdisc, but the new DVD simply credits the song as Closer by Nine Inch Nails. The Criterion laserdisc release also moved a few seconds of Howard Shore's score for its last side break so as to keep the entire music cue intact. The cue plays as originally intended on the special edition DVD.

Depending on the version, the line "Let's finish it" is spoken either by Somerset or Mills.

The film's Canadian Blu-ray release presents the film open-matte, at an aspect ratio of 1.78:1, meaning there was more picture information visible in the top and bottom of the frame than in theaters and on other home video releases, aside from the VHS version.

In the January 2025 IMAX release, Mills' first gunshot at the end is completely uncensored; brain matter and blood are seen exploding in a cloud out of the back of the victim's head. For the theatrical and home releases, this shot was interrupted by a one-second, slow-motion, close-up insert of the gun firing and the slide cycling.

A few hundred of the 2,500 first-run prints released theatrically were created using a silver retention process called CCE. With silver retention the silver leached out during conventional film processing is rebonded to the print, thus greatly increasing luminosity in the light portions of the image and the density of the dark tones.

The writer, Andrew Kevin Walker, completed two separate drafts of the ending. The first is the one that we see, and the second is one where John Doe is killed by Somerset instead of Mills. This alternate ending sequence was storyboarded and is included in the published script, but never filmed.

The version shown on BBC TV in the UK was heavily cut. All f-words were removed, as were some of the more grisly images in the various murder scenes. Most notable cuts were to the autopsy of the 'gluttony' victim (shots of the victims full body as well as the removed stomach are missing) and the interrogation after the 'lust' murder (we no longer see the picture of the implement used in the murder).

The DVD contains an alternate ending which features alternate takes of some scenes. It shows the delivery guy also hand Somerset the truck registration. Afterwards, a wide shot of Mills is shown when John Doe reveals Mills' wife was pregnant, instead of the close up. There is no quick flash of Gwyneth Paltrow's face before Mills shoots Doe, and only one shot to the head is fired. There are no additional shots fired at Doe afterwards.

The US television print is heavily edited for language and violence. Also, there is an alternate shot when John Doe takes the gun away from Mills's head. In the original film, we see a shot of Mills's head with the gun to it, and John Doe's arm. Then the gun is quickly whisked away. In the television edit, we're still looking up the barrel of the gun as it is slowly taken away.