- German theatrical version was based on the cut British version. In addition it was heavily dimmed and cartoon-like sound effects were added to the fight scenes. This version was also used for TV airings and VHS home video releases. Only in 2010 the film was released uncut on DVD.
- A scene during the meeting with Shredder and the Foot Clan, with Shredder fighting two of his students, was cut. For years, the only evidence of this scene was a still image, but the scene has been resurfaced in the documentary, Turtle Power: The Definitive History of the Teenage Mutant Ninja Turtles.
- A redubbed/re-edited version was released in Japan by Towa Video under the "Teenage Mutant Hero Turtles" name which replaced all references to "ninja" with "combat" or "warrior" and "Japan" to "Korea" or "our homeland". Various Japanese-sounding names were replaced with more Korean-sounding names and one shot was even replaced. All scenes depicting Michelangelo's nunchaku remain intact however.
- When aired on the USA Network channel, the scene of Shredder in the back of a garbage truck was edited somewhat. Like in the original version when Casey pulls the lever, the back door closes and the smashing mechanism begins, next shows Shredder's helmet being flattened, in the USA version, now when Casey pulls the lever it shows a scene of the turtles and Splinter watching then a scene of the punks that Casey and Splinter met back at the hideout then cuts to Shredder's helmet being flattened.
- There is an additional scene that was supposed to take place at the end of the movie in which April and Danny go into the offices at Mirage comics to pitch a story about teenage mutant ninja turtles. The publisher turns them away claiming the idea to be too "farfetched" the turtles pop their heads out of each window corner behind the publisher For some reason this bit made it into the book adaptation as well as the sticker book (with pictures), but was left out of the movie.
- The depiction of chainsticks on screen was rarely allowed in the UK, so the movie was heavily cut or reframed to remove every last trace of them for its original theatrical exhibition. In 2003 all these cuts were waived by the BBFC due to changed guidelines.
- In the UK theatrical, television and VHS versions, the ban on nunchuks caused two scene notable scene trims. The face-off in April's apartment in which Michaelangelo and a member of The Foot perform nunchuk moves in succession was removed completely, with the fight starting instead with Donatello diving through the air directly after this sequence. Another sequence trimmed heavily was the apparent death of Shredder. In the full length version, Shredder charges at Splinter, who produces a pair of nunchuks, wraps them around Shredder's staff and hurls him over the edge of the building. Shredder hands onto his staff which Splinter maintains his grip on, and Splinter begins a speech, but is interrupted by Shredder, throwing a scythe at him. Splinter moves to one side, and Shredder looses his grip on the staff, falling into the garbage truck where he is crushed. This was heavily trimmed so that it appears Shredder runs at Splinter, who seemingly trips him up, and Shredder just falls over the edge as Splinter watches on. The original versions of both scenes were reinstated for the 2004 DVD.
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