- For the UK theatrical release, 34 secs were cut from the film to secure a 'PG' rating. The 1993 video version required 1:44 cut to retain the 'PG' rating (including the cinema cuts). The cinema cuts were:
- [Reel 2 / 3 mins] After boy swings from tree at man by car, cut shot of small ninja in tree holding metal stars, and subsequent sight of stars in ground. Resume on sight of old man getting up from ground.
- [Reel 5 / 7½ mins] Remove prominent sight of boys wielding chain sticks in fight with 3 ninjas:
- 1) After boy pulls tube off wall remove all sight of boys improvising chain sticks and brandishing them, resuming on comic episode where ninja inadvertently hits his partner with chain sticks.
- 2) After ninja then rushes towards camera remove high angle long shot of the boys brandishing chain sticks.
- 3) After ninja crashes into fence remove complete sequence of boy in blue shirt and white cap fighting with chain sticks against ninja.
- [At start] In opening titles, remove the dotting of the letter 'i' twice with metal throwing stars.
- [2 mins] After old man is pulled up hill, remove sequence of boy twirling chainsticks while old man throws apples at him and later sight of boy throwing stars at dart board.
- [3 mins] After old man falls to ground, remove sight of boy in tree throwing stars.
- [18 mins] After old man's line ".... between victory and defeat," remove demonstration pinpointing vulnerable parts of the body (throat, groin, etc), resuming on old man telling them to practise for an hour.
- [47 mins] After boy is tossed onto bed, remove sight of him kicking head of man in red cap.
- [48 mins] After man in red cap is pulled through bannisters, remove all further sight of boy climbing up and tying him to bannister rail.
- [62½ mins] Remove all sight of ninjas using chainsticks as follows:
- (1) After ninja wields sword, remove both sights of 3 ninjas with one of them twirling chainsticks.
- (2) After ninjas reel back after being struck by drum, remove sequence of making and displaying chainsticks, resuming on small boy in orange jacket laughing.
- (3) After ninja rushes towards camera, remove high angle shot of boys brandishing and using chainsticks and following shot of boy in blue shirt using them, resuming on ninja with raised sword threatening boy.
- (4) After this shot, remove part of following shot in which boy hits ninja with chainsticks and kicks him on head, resuming as he faces second ninja.
- (5) After ninja crashes into wire netting, remove two shots of boy in blue fighting with chainsticks.
- [65 mins] Reduce fight between two ninjas and boy in white trousers by cutting away after he kicks them to ground and removing later punches to head, resuming on boy in orange.
- [66½ mins] After ninja falls from wall, remove front of shot with punch to head by boy in green.
- [68 mins] When small boy in orange punches large oriental in throat, trim end of punch so it looks as if he only punches him in jaw, and then, after boy in khaki kicks large oriental on head for first time and lights appear on doll, remove kicks to crotch and head, resuming on second large close-up of doll's face.
- [74 mins] After shot of boy in green/blue jacket, remove sight of old man kicking man in red, resuming on long shot before punch to chin.
- The version that airs on the WAM! movie channel has an added scene in which Fester asks his uncle if he can be paid, following the fiasco at the Douglas house.
- The international cut of the film features a number of small parts of scenes that were cut from the movie for its American release, most likely to sure a PG rating. Amongst the cut scenes are [not all-inclusive]: Extra footage of Snyder's escape in which he confronts two FBI agents who he promptly defeats, A scene in which the robbers fire a gun in the convenience store and tie up the clerk behind the counter, a scene in which the robbers get the Douglas family address from Brown, additional footage of Grandpa trailing Snyder to his ship hideout, numerous small portions of the scene where the robbers invade the Douglas household, including Colt beating the robbers after getting them under a tarp in the room being renovated and a scene of one of the robbers asking his uncle (Brown) if he can be paid, extra sarcastic dialogue while the boys are locked up in Snyder's ship, an extended scene in which the boys are reunited with Grandpa, footage of Brown KOing himself on a pipe and subsequently complaining about his pain when being taken away by the Feds. Additionally, in the international version the boys LOSE the basketball challenge and their bikes, so a scene ends the international version of the film in which they fight the bullies to get them back.
- The American version features several scenes/parts of scenes cut (most likely to get a PG rating), and runs several minutes shorter than the international version. In the American version, the boys win the basketball challenge, and the original ending with them fighting the bullies is replaced with an extended version of them driving away with their parents and Grandpa to get pizza, which includes additional narrating/arguing from the boys.
- The German version (3 Ninja Kids) includes an animated opening, then cutting to the narration from the boys, except there's no credits in the narration.
- Global Film Enterprises produced the movie and then gave the distribution rights for certain countries (at least USA and UK) to Touchstone/Buena Vista (Disney). They changed the movie by removing the animated opening credits (instead they put opening credits over the very beginning of the movie and removed some dialogue) and by removing the original end (the day after the showdown Rocky fights one of bad guys at school and wins back his girl friend's, Colt's and his own bike). The German rental video and tv broadcasts show the unchanged movie (and there is no sign of a Touchstone logo). Due to the running time difference (US laserdisc 85 min. vs. German TV 93 min.) there may be more scenes removed by Touchstone.
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