Originally, there were several nods to real world products such as Marlboro Cigarettes, Agip Gasoline, Mobil1 Oil, Goodyear, and 76 Gas Station. They were altered internationally for two likely reasons; One of the companies parodied sold cigarettes (possible trouble for an E rated game) and any of them could have sued.

In its early beta stage, the game was known as Super Mario Kart R. Some differences were Kamek as a playable character who would later be replaced with Donkey Kong. Also there was an option to have the multiplayer screen set to horizontally or vertically, but this was removed in the final version. A number of other small differences were the avatars in the "Character Select" screen, the textures of the "Item Boxes", the feather as an item, and other minor graphic details.

Letting the music on the results screen loop 64 times (roughly 50 minutes) causes the music to change, playing an alternate hidden version of the "results" theme.

If the player places 4th or 5th overall in a Grand Prix, they will be shown a cutscene where their character looks on at the winners, sadly drives off, and then gets blown-up by a Bob-Omb. The game then shows a message that says "What a Pity! You placed 4th/5th; Maybe next time!" Throughout the cutscene, the music changes from the standard fanfare to a more bleak version when the losing character drives off, and soon slows to a stop when the Bob-Omb appears.

If the player places in the top three, it's also possible to see the 4th place character in the distance for a brief moment, alluding to the hidden cutscene.

The voice clips for each of the menu options in the Japanese version of the game are in English, but the speaker has an inconsistent accent, and emphasizes each word in an unnatural manner. These voiceovers were replaced with Mario's voice in the international releases.

Luigi, Peach, Toad and Wario's voices were changed in the Western releases of the game from those used in the original Japanese version, which were already in English done by non-English speaking voice actors. It's thought that Nintendo of America felt the original voice clips did not properly represent the characters, or were simply of poor quality. However, the original Japanese voices were later used in the first two Mario Party games in the worldwide releases, as well as Mario Kart: Super Circuit.

Charles Martinet's name is misspelled "Charles Martinee" in the credits of the Japanese version.

Twice as many people are credited as voice actors in the Japanese version compared to the American version, with Charles Martinet being the only one to provide voices for both versions of the game.

Thwomp's laugh is actually Wario's laugh slowed down. Since Wario's original voice from the Japanese release was changed in the Western version to sound more fitting, Thwomp's voice was also affected.

The Game originally had a Vertical Split-screen in 2 Player gameplay. This cannot be done without hacking in the Final Version, and the Lap Counter still appears in Battle Mode. Mario Kart 8 later managed to use Vertical Split-screen 18 years later.

In the Virtual Console versions, the lightning power-up's visuals were changed to reduce the intensity of the flash. This was likely done to avoid causing seizures.

The Japanese version The course "Moo Moo Farm" is called "Moh Moh Farm". This is because the Japanese onomatopoeia for mooing sounds like "mo͞o", with a long "O" sound.

The trophy ceremony in the Japanese version displays the text "You are in (position)". The American version changes this to "You placed (position)". The punctuation was also removed.

The idea for the Blue Shell came to mind after processing limitations prevented the developers from showing all of the characters on screen at the same time. Their solution was to clear an overcrowded track with using the Blue Shell.

In the "Big Donut" battle stage, there are 2 hidden item boxes that can be seen under the track. They're inaccessible, and were likely just left over from development.

Due to the complex maze-like structure of Yoshi Valley, the HUD’s mugshot are reduced to question marks, and the player’s position in the race doesn’t appear at all.

This error would be eventually mostly fixed when the track reappeared in Mario Kart 8 and Mario Kart Tour, although some items like the Red and Blue Shells, occasionally, may miss the character in front of the player.

In the Chinese port for the iQue Player, the 'Special Cup' has been renamed 'iQue Cup', though the courses appear to the same.

In the Japanese version of Mario Kart 64, instead of the announcer and menu options being voiced by Mario they are instead voiced by the same VA who played the announcer in Wave Race 64: John Hulaton.

According to Hulaton in an interview with DidYouKnowGaming?, after recording his lines for Wave Race 64 he was handed a slip of paper and was then told to record the lines on it without being told what it was for. These lines ended up being for Mario Kart 64. Hulaton's agent was reportedly very upset, as Hulaton was not paid for these lines and on top of that his name was misspelled as 'John Huraton' in the credits.

The lines he recorded would then later be used in the Japanese and International versions of Mario Kart: Super Circuit, where he remained uncredited.

At the end of each cup, the Award Ceremony for the top three racers in the cup is held outside Peach's Castle as it is seen in Super Mario 64. This is not a unique, inaccessible area, but can actually be found in Royal Raceway, popularly featuring an open pathway allowing you to drive around the starting area of Super Mario 64. However, this area is also not a shortcut and you must return to the racetrack if you want to continue the race. Alternatively, you can fall in the castle's moat, causing Lakitu to pull you out and return you to the racetrack.

On Toad's Turnpike, the bus is driven by what many have assumed to be the silhouette of Diddy Kong. On the Mario Kart 64 Japanese website, it is instead stated to be a Ukiki wearing a hat.