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. 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.

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.

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.

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.

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.

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