Aside from owl saves, the American release of Majora's Mask had a number of other changes made to it, both aesthetically and to its game-play, such as making dungeons easier, or simply moving objects around.

The impermanent flow of time in the first three-day cycle as Deku Link is 1.66 times faster than normal, meaning it takes only 27 seconds for each game hour to pass rather than the standard 45 seconds for every three-day cycle after it. It is in this stage of the game where NPCs and most enemies are not rendered outside of Clock Town's boundaries.

The aliens that attack Romani Ranch during the first night are based on the Flatwoods Monster, an alledged alien being that was reported to have been sighted in the town of Flatwoods, West Virginia, USA, on 1952.

The Song of Healing has the same first six notes as Saria's song but played backwards with a different rhythm.

According to the gossip stone in Romani Ranch in the Cucco Shack, the All-Night Mask was used as a torture device.

"A torture device of insomnia called the All-Night Mask seems to be available at the Curiosity Shop..."

When the thief Sakon tries to steal the bomb bag from the Old Lady from the Bomb Shop, if Link hits the Bomb bag with an arrow, the hookshot, or another bomb, the bag will explode, killing Sakon.

At the end of the game, Skull Kid asks Link to be his friend and says, "You have the same smell as the fairy kid who taught me that song in the woods." This hints at the Skull Kid being the same one that Link sold the Skull mask to and taught Saria's song in Ocarina of Time.

The arch at the entrance to Romani Ranch is actually the same arch at the entrance to Kakariko Village from Ocarina of Time. Even the text on the sign is re-used, effectively saying "Welcome to Kakariko Village" in both games. This is more noticable in the Japanese version, which features the text in Japanese instead of the localized version's Hylian text. The Hylian text still translates to "Welcome to Kakariko Village", though.

If Link is wearing the Captain's Hat during the fight with Igos du Ikana, a cutscene will take place where he will mistake Link for Captain Keeta, a military general for the Ikana. He then realizes that Link is too tiny to be Keeta and then resumes attacking Link.

If the player equips the Bremen Mask and plays the marching melody during the Ikana Warriors mini boss battle, they will march with Link. It's quite handy to leave them open for an attack. However, it won't work with the following mini boss, Igos du Ikana, as he'll just attack Link regularly.

During development, Majora's Mask went by the name Zelda Gaiden. It was being developed for the failed Nintendo 64 Disk Drive add-on, and was to take full advantage of the hardware. The player originally had seven days to complete the game rather than three and it used the Disk Drive's internal clock to play out in real time.

In a prerelease trailer for Majora's Mask, there seems to be an unused mask that looks like Adult Link for Ocarina of Time. This mask was rumored to be a transforming mask which would turn Link into Adult Link, allowing him to use certain items. The mask was removed before the final version and young Link is capable of using all of the items directly.

If Link is wearing the Garo's Mask, the Gibdo Mask, or the Captain's Hat in the presence of Redeads, they will start dancing.

In the Astral Observatory, there is a picture of a dolphin hidden under a small pot. It's thought to be a reference to Dolphin, the Gamecube's code name at the time.

The development for Majora's Mask started out of a lack of enthusiasm to work on the unreleased expansion for Ocarina of Time for the Nintendo 64 Disc Drive, dubbed "Ura Zelda". Eiji Aonuma protested the expansion, so Shigeru Miyamoto challenged him to make a sequel for the game within 1 year, in exchange, they would no longer have to make Ura Zelda.

In the game, there are unused cutscenes that show the Great Fairy training Link for his new abilities instead of just magically giving them to him.

Although Majora's Mask is a direct sequel to Ocarina of Time, there was an officially licensed novel released set shortly after the events of Ocarina of Time. "Link and the Portal of Doom" was written by Tracey West and published by Scholastic in 2006 as part of the Nintendo Heroes series.

In the book, a mysterious portal suddenly appears in Hyrule which absorbs all things around it and threatens to destroy the land. Link and Navi have to travel across Hyrule to learn five parts of a song which will destroy the portal.

Although officially licensed by Nintendo, it's considered to be non-canon.

Majora's Mask contains a reference to the Star Fox characters. The masks on the second row of the mask screen resemble the same animals that the Star Fox team is based on, including one of their enemies, a former member of their team who betrayed them.

In order:
• Keaton Mask = Fox
• Bremen Mask = Falco
• Bunny Hood = Peppy
• Don Gero's Mask = Slippy
• Mask of Scents = Pigma

At one point in the Spirit Temple in The Legend of Zelda: Ocarina of Time, Link must fight an Iron Knuckle that turns out to be a hypnotized Nabooru, who returns to her senses after being defeated. By clipping the camera through her Iron Knuckle armor, you can see her head modeled underneath her helmet, likely to facilitate the post-defeat cutscene where her armor falls off.

Furthermore, every other Iron Knuckle in the game also has a placeholder Gerudo head modeled underneath the helmet. While much of the head's face is obscured by chainmail, the details that are present indicate that it is most likely an early version of Nabooru's design; of note is that the head's hairstyle is closer to that seen on Gerudo Village's guards, implying that this element was reused for them when Nabooru's design was revised to the version seen in the final game.

This placeholder head is also present inside the Iron Knuckles that Link encounters in The Legend of Zelda: Majora's Mask, due to that game reusing many assets from Ocarina of Time.

During day 3 at the Romani Ranch, you can trigger a conversation where Romani tells you that that night is finally the night when she gets to drink Chateau Romani. According to the sisters, the properties of Chateau Romani are so potent that children aren't allowed to drink it under normal circumstances, drawing parallels with alcohol in the real world. It's also only served in the Milk Bar, where children aren't allowed, and is only open at night. The scene at the ranch unfolds with Cremia stating that she acknowledges Romani's adulthood, and asks her little sister to sleep in her bed tonight. Cremia dishearteningly utters "See you... Tomorrow... OK?" while Romani cheerfully adds "See you tomorrow!"

It seems as though Cremia knows that they're about to die, and is giving Romani the drink to dull her senses, so that she remains blissfully unaware of their destruction.