In the original Japanese version, if the player runs to where a key will land after defeating Bowser in the Dark World or Fire Sea, presses C-Up and looks somewhere, Mario will keep looking in that direction during the key collection cutscene.

There is an unused animated Yoshi egg texture in the game's data, suggesting that Yoshi was going to play a bigger role in the game, similar to Super Mario World.

In 1997, Nintendo released a Japan-exclusive version of Super Mario 64 which had Rumble Pak support. It also included the English voice acting which the original Japanese version didn't have, and fixed some glitches. This version would later see an international release when Super Mario 64 was included in Super Mario 3D All-Stars.

If you allow Mario to fall asleep (by remaining idle for an extended period of time) for long enough, he'll start sleep-talking about spaghetti and ravioli, two Italian foods.

The enemy Blargg from Super Mario World is found in the game's code, but it's model and programming are unfinished. It has an animation for jumping out of lava, but doesn't do anything else.

The Big Boo in Big Boo's Haunt course originally held a key instead of a Power Star inside of him. The keys would unlock the various doors in Big Boo's Haunt. There was even a key counter to display how many keys the player had acquired.

Early in development, there was originally going to be a level-cleared flagpole. However, the developers felt that scouring the land for hidden items was better, so the flagpole was scrapped. It would later be included in Super Mario 3D Land, and Super Mario 3D World.

Several of Mario's voiced lines didn't exist in the original Japanese version of the game, and were added for western releases:

• "Hello" and "Press Start to Play" during the demo screen with Mario's head.
• "Okey-dokey!" when choosing a save file.
• "Let's-a go!" when choosing a star.
• "Game over." when Mario runs out of lives.
• His dreams about pasta are missing.
• "I'm-a tired." - when the player is idle.
• "So long-a Bowser!" - when Mario throws Bowser a long distance.
• "D'oh!" - when long-jumping, sliding, or diving into a wall.
• "Boing!" - when bouncing off of a Spindrift's head.
• Mario will say either "Yahoo!", "Wha-ha!", or "Yippee!" during the last jump in a triple jump. In the Japanese game, he says "Yahoo!" every time for the third jump.
• In the opening sequence, Mario says "Yahoo! Ha ha!" when he leaps out of the pipe instead of just "Yahoo!" in the Japanese version.
• Mario will always say "Mama Mia!" after being ejected from a level's entrance after losing a life, unlike the Japanese version where he only says it when ejected from a portrait.

Princess Peach doesn't have any voice acting in the original Japanese release during the beginning and final cutscenes. This was added for all other versions.

The second Power Star on Cool Cool Mountain, acquired by reuniting the baby penguin with her mother, appeared over the mother penguin's head in the Japanese version. It was moved next to the pool in other releases, likely to make it easier to obtain.

Two small Koopa Troopa shells, one green and one red, can be found in the game's data. Both of these shells are the same sizes as Spiny shells, however, they cannot be used.

There is a glitch that causes Mario to hold his hat in his right hand. This occurs when Mario picks up two hats in rapid succession. If Mario loses his hat in Snowman's Land by being blown away by the giant snowman's breath, and then takes the warp under the tree, his hat will duplicate, and retrieving it will cause this glitch.

There is a metal wing texture in the game for combining the Wing Cap and Metal Cap, similar to how the Vanish Cap and Metal Cap can be combined in Dire Dire Docks and Wet Dry World. There are no levels in the game where it would be possible to equip both simultaneously, but they do function and use this texture if given to Mario via hacking.

In the mission "Blast to the Stone Pillar" in Jolly Roger Bay, the Power Star is contained within a box in the Western versions of the original game, but not in the Japanese version. This was likely changed during localization to make the star's position less obvious. However, all versions of the Nintendo DS remake leave the Power Star out in the open.

Early in development, before Charles Martinet was hired to provide Mario's voice, the developers used stock Looney Tunes voices as placeholders.

The Japan-only Shindou Pak Taiou edition of the game contains an exclusive Easter Egg on the introductory screen: pressing Z fills the background with images of Mario's face. These images are taken from the frame buffer, and therefore reflect the current state of the 3D model of Mario's head that the player can manipulate.

In the world "Bowser in the Sky", two Goombas can be seen on the same platform together. These two Goombas are actually part of a Goomba trio object loaded by the game, however, the third Goomba is placed over the edge of the platform, resulting in it rendering at the bottom of the stage, out of reach.

An unused trampoline can be found in the game's files. It has no model in-game, and behaviour for it was never created.

The enemy "Whomp" was likely inspired by a Japanese mythological creature known as a "Nurikabe". Nurikabe were said to take the form of a wall either to trick or trap any travelers. It's also said that Nurikabe could expand infinitely in size. The only known way to make it disappear was to knock on its lower-right-hand side.

In a late pre-release build, stars that have already been collected are in grey shades instead of the dark blue seen in the final version. This was shown during E3 '96 when demonstrating the game before its release.