- Originally, at the end of the Japanese version of World 5-1, you would go through the pipe. You would emerge on the other side of the wall, and would find the goal area after about 20 more blocks of vacant terrain. This ending was shortened in the U.S. version, as the "darkness" was moved ahead to where the pipe and wall used to be. The wall was removed to fix an odd, harmless glitch that would happen if you were to fly over the wall after going through the pipe.
- The original Japanese version of this game featured several differences from the version of the game that would later be released in North America and Europe. In the Japanese game, Mario always reverts back to small Mario when he is hit, but in the American version he'll change to Super Mario if he is hit while he has a power-up. Peach's joke at the end of the American/PAL version was added in (the original Japanese text simply said, "Thank you! Finally, peace returns to the Mushroom World. The end!") The Japanese version of the game featured different levels names than (most) versions of the American/PAL game (Desert Hill became Desert Land, Ocean Side became Water Land, Big Island became Giant Land, The Sky became Sky Land, Iced Land because Ice Land, Pipe Maze became Pipe Land, and Castle of Kuppa became Dark Land). There were other small changes made as well to specific levels (the end of the Grass Land fortress was slightly altered, as was a level in World 5).
- Was re-released as part of Super Mario All-Stars. The version of the game featured here is a mixture of the Japanese and American/PAL versions, with 16-bit graphics. For instance, the Japanese level names were used, as were a few graphic effects omitted in the American/PAL versions. The changes to level design made for the American/PAL version remained in tact.
- Re-released in 2003 as Super Mario Advance 4: Super Mario Bros. 3 for Game Boy Advance. The game allowed players to save their progress at any point in play, and also altered some levels to make them slightly easier. If players owned an e-Reader, they could access special levels made especially for the Game Boy Advance, or access power-ups at any point during gameplay (including Super Mario World's Feather, which wasn't in the original game).
- Nintendo of America released two different American versions of this game. The following is a list of the changes made to the first version:
- The original Japanese world names, which were used originally were changed to the following:
- "Desert Hill" became "Desert Land".
- "Ocean Side" became "Water Land".
- "Big Island" became "Giant Land".
- "The Sky" became "Sky Land".
- "Iced Land" became "Ice Land".
- "Pipe Maze" became "Pipe Land".
- "Castle of Koopa" became "Dark Land".
- A grammatical error present in Toad's N-Spades game, "Miss twice and your out!" was corrected and changed to "You can only miss twice!" in order to fit the screen.
- "Kuribo", the original Japanese name for "Goomba" was changed to the latter in the World 2 letter from Princess Toadstool.
- The game was re-released with these changes made, and most copies of the game are of the second version.
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