At the beginning of the game, you come across a warped dead Deku like figure. We can presume that this Deku scrub died in a horrible way. Additionally, later in the game, the Deku butler directly states that Link reminds him of his son, and he is seen weeping over the figure in the end credits. It's likely that this figure is the butler's son, and his spirit has been with you throughout the whole game.

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.

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.

The Legend of Zelda: Majora's Mask contains a reference to the Star Fox characters. The masks on the second row of the masks 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

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.

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 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.

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 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.

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.

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 Japanese version of Majora's Mask contained three save slots as opposed to the two that the American release saw. However, in the Japanese version, the owl saving feature did not exist, making the Song of Time the only way to save. This proved to be annoying and owl saving was added to the American release, at the cost of one save slot.

A clear impression of Skull Kid can be seen in the grass when looking towards the south entrance of Clock Town from the Astral Observatory telescope.

"Farewell to Gibdos" has a similar melody to that of the Merry-Go-Round located at Big Boo's Haunt in Super Mario 64.

In the magic hag's potion shop, Kotake is standing on a box of lemons in order to reach over the counter.

Majora's Mask was planned for release on the iQue Player, a Chinese version of the N64, and there are several screen captures from the game on the back of the iQue packaging. It's theorized that the game's dark undertones and imagery were deemed too violent to pass Chinese censorship laws, so the release was cancelled.

Though not explicitly stated in the game, the instruction booklet mentions Termina as a kind of parallel world of Hyrule.

All 4 main dungeon items pertain to the Bow. Woodfall Temple features the bow itself, while the Snowhead Temple has Fire Arrows, the Great Bay Temple has Ice Arrows, and the Stone Tower Temple has Light Arrows.

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.

During an early Beta version of Majora's Mask, the Fairy Ocarina was available and usable.