The Japanese and European versions have a short animation of the level timers getting sucked inside doors along with Mario to make it more clear that the player's remaining time carries over. This does not happen in the US version.

The US version of the game featured e-Reader support. The support would allow players to scan 5 different cards to unlock 5 new levels. This was not widely known as only 1000 of the card packs were produced and given away as part of a special promotion. The European release of the game had the feature removed completely.

The game started out as 'Donkey Kong Plus', a sequel to the Game Boy Donkey Kong with updated graphics and a level editor. This was even shown at E3 in 2002. The game was scrapped, but was recycled with the inclusion of mini Marios. The game was then re-named Mario vs. Donkey Kong.

Nintendo originally planned to include a level editor in the game. The level editor is still in the game's code, and by editing the game's memory, the level editor can still be accessed.