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.

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.

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.

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.

The Idea for Metal Mario may have come from an interview with Shigeru Miyamoto published in 1991, in Nintendo Power's Mario Mania Player's Guide, Miyamoto reportedly said: "Who knows what Mario will look like in the future? Maybe he'll wear metallic clothes!"

In an interview with Satoru Iwata and Shigeru Miyamoto, it was revealed that an early, experimental build of the game had split-screen multiplayer, with Mario and Luigi as playable characters.

The game's planned multiplayer mode ended up being reworked into a Mario Bros.-style minigame thanks to the Nintendo 64's technical limitations making the split-screen concept unfeasible. However, in February of 1996 (just a month before E3 of that year), both multiplayer mode and Luigi were removed, in part because the Nintendo 64 was bundled with only one controller. These statements are corroborated by findings from the Gigaleak, a massive content leak of internal data from Nintendo in 2020 that included early assets from Super Mario 64. Among the leaked material was a model and textures for Luigi and sprites for "1P" and "2P" icons. Luigi's model is dated June 20, 1995, while the icons use the same generic font seen in the Shoshinkai demo from November of that year, rather than the custom font seen in both the E3 1996 demo and the final release.

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.

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.

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.

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.

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 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.

If you jump up and down in a shallow pool of water, you can occasionally see a fish jump out of the water with you.

As early as January 1997, a cancelled sequel for Super Mario 64 was in development, commonly called "Super Mario 64 2" or "Super Mario 128" (not to be confused with the tech demo of the same name) for the failed Nintendo 64DD expansion. Only one demo was ever made, but was never shown to the public. Luigi was planned to feature in it as a playable character, and anywhere from two to four player co-operative play was planned. Shigeru Miyamoto once said he hoped to make the game as complex as Banjo-Kazooie, and joked that the box art for the game would be green if the demand was strong enough for Luigi.

MIPS, the rabbit in the castle basement, is named after the MIPS (Microprocessor without Interlocked Pipeline Stages) microprocessor. The Nintendo 64's CPU runs on a MIPS Microprocessor, so the name was chosen for the rabbit.

In early development of the game when Nintendo were working on character movement and camera angles, they only had two characters; MIPS the rabbit and Mario. MIPS was planned to be just a testing dummy, but made it into the final game because they didn't want to part with him.

When you catch MIPS the bunny in the castle basement, he references Alice In Wonderland. Just like the White Rabbit, he says he's late. Then he says says he'll give you a star, but he has an important date to get to.

The penguin found during the 3rd star of the "Cool, Cool Mountain" level changes after 120 stars are found. After obtaining all the stars, the penguin is found much fatter than before from not doing races lately. He can be raced again, but there is no additional reward for beating him.

There are murals on the pillars in Bowser in the Sky depicting the original fight with Bowser from Super Mario Bros.

In the Japanese version of the original game, the painting for Jolly Roger Bay originally had a blue frame with bubbles. This was changed to a pirate ship with a gold frame in the international release of the original game. In the Nintendo DS remake, the painting reverted back to the original blue-framed form.