A popular internet joke upon the release of Super Mario 64 was "What happened to Super Mario 4 through 63?" If one is to calculate every Mario game released before Super Mario 64, including outliers such as ports and titles not released on Nintendo hardware like Mario Teaches Typing, the game would be the 113th title on the series. However, if you were to only count games released on non-devoted Nintendo hardware and remove ports, the title would be, very anti-climactically, the 63rd Mario game.

The audio used for Bob-ombs, Monty Moles and Goombas in various games starting with Super Mario 64 is actually pieces of Mario's voice saying "Here We Go" from said game after being pitch-shifted. This would continue being the case even after Charles Martinet was replaced with Kevin Afghani starting with Super Mario Bros. Wonder.

The title of "first 3D platformer" is often erroneously given to either 1996's Super Mario 64 or 1995's Jumping Flash!. Despite this, neither game can factually claim that title, with 1990's Alpha Waves being the true owner of the title according to Guinness World Records.

Additionally, 1984's I, Robot - while primarily a shooting game - did feature 3D platforming segments.

In the castle courtyard in Super Mario 64, there is a plaque to a power star with an illegible name written below, often interpreted as either "Eternal Star" or "L is Real 2401" - with the latter being more popular for how it could be seen as a cryptic hint towards unlocking Luigi.

In a poetic coincidence, the source code leak that revealed Luigi's scrapped model would be found 24 years and 1 month after Super Mario 64's release.

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.

Although the Headless Snowman is a minor character in his few appearances, he received some publicity in the form of a Nintendo Power joke published around the time of the main circulation of the "L is Real 2401" Super Mario 64 rumors.

In Volume 107 of Nintendo Power, in the April Fool's-themed "April News Briefs" segment, a "Luigi 64" article is present, where Nintendo states that Luigi fans had been campaigning to have the character in his very own game, and the company's response was to create a hoax upcoming game known as "Headless Snowman 64". This game was apparently intended to satisfy fans of the "second bananas" by featuring a cast of both well-known and obscure Nintendo characters, with the obscure characters including the Wave Race 64 announcer, "random audience members from Super Punch-Out!!", "the frogs in the meadow" from Diddy Kong Racing, and the Headless Snowman himself. Additionally, the game would supposedly contain some non-Nintendo characters such as "that bald guy from Blast Corps," and "the bikini woman in Cruis'n USA." Humorously, this never-made game was not going to feature Luigi, with a developer comment at the end of the article confusing him for "one of the civilian women in GoldenEye 007".

In a 1996 interview with Shigeru Miyamoto published in Super Mario 64's first Japanese strategy guides, he revealed that Mario's running animation, speed and movements in that game were influenced by Arale, the main protagonist of the 1980 Akira Toriyama manga/anime "Dr. Slump":


However, Dr. Slump's influence throughout the Mario series could trace back even further. Some particular examples from Mario games include:

• His running speed, animation, the Racoon and Tanooki Suits from Super Mario Bros. 3
• The Wing Cap from Super Mario 64
• The Cat Suit from Super Mario 3D World

Even traits of Mario's happy cartoonish personality, his short stature and gloves, and blue-red-overalls color scheme bear enough similarities that they all could have been taken from Arale's appearances and other elements throughout Dr. Slump. Despite this, outside of Miyamoto's comment, these connections are not known to have been elaborated on by any other employee from Nintendo.

A rideable horse was discussed during early development of the game but was never included. This idea eventually made it into The Legend of Zelda: Ocarina of Time as Link's horse, Epona.

In addition to the red, blue, and green switches, there was originally going to be a yellow switch too. When used in game, the switch is automatically set to the "on" position for unknown reasons.

After defeating Bowser, a key will appear with a number of coins flying outwards from it, but none of them actually fall onto the ground. This is likely a remnant of a past idea where coins would appear after Bowser's defeat, as seen in early pre-release footage. The idea was likely scrapped as the coins would serve little to no purpose after defeating Bowser, since Mario's health automatically recovers after collecting the key and returning to the hub world.

In early version of the game Mario's health bar was different. It featured numbers, as well three colors, green, yellow and red. This was later changed in the finished product where Mario's health is a full pie graph, and the colors that are in the final version of the health bar are Blue, Green, Yellow, and Red.

There's unused text that may have been spoken by a Boo upon entering Big Boo's Haunt, saying "Eh he he... You're mine, now, hee hee! I'll pass right through this wall. Can you do that? Heh, heh, heh!" It was likely removed because no mission involved chasing a Boo through the Level.

If you pick up Tuxie the baby penguin after returning her to her mother, the mother penguin will angrily follow Mario around until Tuxie is put back down.

The "Slider" and "Snow Mountain" Theme are both variations of the main theme of Super Mario 64, which is played on the "Bob-omb Battlefield". The songs are all played at different tempos and with different instruments, but are largely the same tune.

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.

There is an unused flower within the graphics for Lethal Lava Land.

The Wing Cap theme is actually the "Powerful Baby" theme from Super Mario World 2: Yoshi's Island, but sped up and featuring different instruments.

During a stream of Super Mario 64, Twitch user DOTA_Teabag accidentally warped upwards in Tick-Tock Clock while trying to land on a platform on the first floor. While similar to a glitch in Bowser in the Fire Sea that allows Mario to warp into the caged portion of the level from the platform directly below, DOTA_Teabag's version did not rely on any hang-able ceilings being above Mario during its performance. This prompted Super Mario 64 analyst and Youtube personality Pannenkoek2012 to offer a $1000 reward to anyone who could submit a recording of themselves replicating the glitch in Mupen64 (a Nintendo 64 emulator) under the same criteria as when DOTA_Teabag discovered the glitch, with the purpose of reverse-engineering it.
At the time of this writing the bounty has not been collected.

The level select sound that occurs after the player jumps into a painting is actually the first few notes of the Super Mario Bros. overworld theme but with vocals.

The concept of a floating Mario head on the title screen was taken from a prototype of a game called Mario Paint 3D. It is unknown what this game was going to be but it was speculated to have eventually become Mario Artist Paint Studio for the 64DD.