- In the Italian release, the ending is cut so Mario and Luigi don't go back to Brooklyn.
- The UK cut has different amount of both songs that appear in the end credits. The first song starts when the actual credits begin. Also "Distributed by Buena Vista Distribution, Inc." is missing in the very end and "Hollywood Pictures Presents" in the beginning (Distributed by Entertainment Films Distributors in UK)
- In 2015, Discovery Family aired the film. Some scenes were edited/omitted because of time and content.
- After Mario throws Luigi the water bottle, there's a wide shot of NYC that's been removed.
- There's a commercial break, so the establishing NYC night shot before the Bella Napoli dinner scene is gone.
- In the flooded construction site, Iggy and Spike's conversation after "What percent is that?" is cut out.
- It cuts to Mario asking for Luigi's hand, cutting out the fun bit with him fixing the leak with multiple tools.
- preparing some fried Tweeter on a bun.
- After Big Bertha steals the rock, her Thwomp Stomper escape is missing the landing in the central walkway before stomping off again.
- In the worst cut so far, Toad's entire monologue about parallel dimensions is gone.
- Koopa: "Goomba." Toad's "Ahhh" response is gone.
- Koopa: "Your de-evolution will be a living nightmare if you don't tell me where that meteorite piece is" is cut.
- The prison escape sequences with cheering inmates is chopped down quite a bit.
- Police Chase alteration--the shots on and around Luigi's: "Hey Mario, you're going the wrong way!" are gone.
- Koopa: "Do you know what I love about mud?" lines are cut.
- Iggy/Spike wanting to formulate their own strategy, "tete-a-tete, inner circle" lines are cut.
- The wide shot of Dinohattan is gone, as well as the following Daisy/Yoshi scene.
- Mario/Luigi using the Snifit masks to sneak past security is gone. It cuts straight to the Boom Boom Bar after the fight scene.
- Mario "acquiring" the crystal from Bertha is trimmed down, likely to make it less risqué.
- Mario and Luigi's "impossible" conversation in the Sludge Gulper is gone.
- Koopa's scene with Daisy's father is cut short for a commercial, and it picks back up after it's over with Mario & Luigi.
- Lena's "If not with you, then on my own" conversation with Koopa is cut, making her storyline pretty confusing afterwards.
- The scene where Luigi begins to make the Goombas dance is cut in half.
- The dancing Goombas being interrupted by their higher-ranking officer is trimmed down.
- In another painful cut, Luigi's "Luigi Mario, you got a problem with that?" line has been removed.
- Mario's "come and get it, ruffle-head" scene is cut so they can only show one shot of the Bob-Omb falling through the foundation.
- After the merge back to Dinohattan, you won't see the Bob-Omb and the clown shoes guy.
- The "Super Mario Bros." logo is missing from the end of the film.
- On June 1, 2021, a restored Extended Cut of the film was released online by fans on Super Mario Bros. The Movie Archive. The Extended Cut is about 20 minutes longer than the theatrical version.
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