- The Blu-ray and digital platform used the short version of the 2003 Warner Bros. Family Entertainment logo with the 1996 crunching noises while the last few seconds of the fanfare is played twice when in fact it should've ended once.
- Following attacks from politicians on violent films aimed at children, Warner Brothers. pushed the release date back and recut the film to a tamer version, toning down some of the violence in the original cut sent out in screener tapes. On April 23, 2001, the unedited version of the film was released in the US exclusively on DVD. Up until that point the uncut version had only been released as screeners that were sent out before the changes were made. The following are scenes that were changed in the edited-for-content version:
- Lots of white flashes have been added to the action sequences where there were previously none. Additionally, combinations of punches have been mostly trimmed down to one punch. For example, Woof slashes the guard once now instead of twice. Batman no longer punches Ghoul in the gut, he just uppercuts him into the dish. Later on in the club, Terry's vicious attack on Ghoul is cut to a flash and Terry running away while Ghoul falls. There is a 360-degree fight sequence in the opening battle that has also been removed, where Batman fends off the Jokerz one by one.
- Seat belts added to Terry and Bruce as the drive home after their first meeting with the new Joker.
- Bonk is not shot, but given a lethal dose of laughing gas, and he dies off screen. Because of this the whole "Take the trash outside, Dee Dee" and "Are you with me?" sequence is cut.
- When Bruce throws the batarang it appears as though he's pleased he can still throw & catch a batarang instead of it showing him using it to decapitate a Two Face dummy.
- When Terry enters the Batcave to find it demolished by the Joker, the letter's 'HA! HA!' written across the floor are changed from red to purple. Probably to assure us it is not written on Bruce's blood.
- All other blood is removed. (Only one example was passed over. In the flashback sequence when Batman smashes through the projection he smacks the Joker. Blots of blood fly from the Jokers mouth, but he is not bleeding in the next shot.)
- In the unedited version, when Batman (in the present) frees himself from the Jokers' ribbon wrap, he throws the knife that he used to free himself with at the Joker. The Joker ducks at the last second and the blade goes through the stage curtain. This would explain the hole behind the Joker.
- The Joker is not shot, but slips in some water and is electrocuted off screen. Plus, they don't mention they buried him deep under Arkham or any of that. The dialogue is completely changed in that sequence.
- Barbara says that Leslie Thompkins helped Tim Drake "regain himself" instead of "regain his sanity." (or something along those lines)
- During a montage where Batman and Batgirl comb "the underworld" looking for clues about Robin's disappearance, Batgirl talks to a nicely-dressed man and woman instead of two sleazily-dressed women (who are pretty obviously hookers) on a street corner.
- Also, Joker no longer slices Batman across the chest of in the leg, and any blood is digitally removed. Joker just punches Batman.
- More than half of the "Our Family Memories" is cut out, only showing Robin tied up and struggling, and cutting the scene where Joker opens the barbeque lids, picks up the voltage tongs, and shocks the Boy.
- A lot of dialogue is changed as well. And reference to the word "kill" is changed.
- The opening fight seqeunce is trimmed, cutting out a second Dee-Dee kick and completely redoing that entire Batman/Dee Dee sequence.
- The club fight is changed. The pink clown no longer punches Terry and says "I don't know why the boss wants a dreg like you outta the way, but as long as it's fun...". He just goes for his gun and says "Slag him!".
- Bruce says "Robin defeated him." instead of "Robin did kill him". Joker says "Bat-Kook" instead of "Bat-Fart". Jordan Price says "Ice" instead of "kill". Tim Drake says "I can still hear his scream" instead of "I can still hear the shot". Joker says "...with such yutzes" instead of "...with such putzes".
- In the scene where the satellite laser chases the Batmoblie it blasts an unmarked, dark, seemingly empty building. Originally it was a lit movie theater. (In the edited version the word 'cineplex' can be seen exploding out of the wreckage in the last few frames of the shot.)
- The clothing on 'Nanna Harley' is changed from blue and purple to Harley Quinn's trademark red and black.
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