After playing the Song of Soaring, the map that displays locations Link can travel to comes up. The locations of the Southern Swamp and Windfall are displayed incorrectly. The Southern Swamp is shown to be east of Woodfall, but the player must travel east from the Southern Swamp in order to go to the Old Hags Potion Shop, Deku Palace and Woodfall.
This was corrected in the 3DS remake.

During early trailers of the game Zora link, Deku Link and Goron Link had their instrument icons instead of the ocarina. It's unknown why this feature went unused in the original game but it was later reused in the 3DS remake.

After Kafei gives Link the Pendant of Memories, he asks Link to keep it "a secret to everybody", a reference to the popular quote from The Legend of Zelda.

One possible reference in the game occurs during the final boss fight against Majora's Incarnation; he sometimes hums what sounds like the melody to the Death Mountain Dungeon from the very first Legend of Zelda

Zelda was originally going to use a flute to teach Link the song of time, but the instrument was swapped for an ocarina.

An unused fishing mini game can be found in the game's data. It would have been similar to that of the fishing in Ocarina of Time. Fish and the owner of the fishing mini game can be spawned into the game by modifying the data, but using the fishing rod will frequently cause the game to crash.

In the North American commercial, a woman can be heard saying "Though I walk through the valley of death, I shall fear no evil."

This is a paraphrasing of the first half of the Bible verse Psalms 23:4, "Yes, though I walk through the valley of the shadow of death, I will fear no evil: for you are with me; your rod and your staff they comfort me."

Inside the moon, there is a bird that flies around the tree on the plain. This bird was originally in the beta version of Ocarina of Time, but went unused and was repurposed for Majora's Mask.

There's unused text regarding getting a seahorse in a bottle. In the final game, the player must have an empty bottle to get a seahorse.

"You traded for the Seahorse.
And it came in a bottle!
You should hurry and return it
to its home at Pinnacle Rock."

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

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.

The five main areas mirror the five stages of grief.

Clock Town is denial; its residents continue their daily lives refusing to believe the moon will fall.

Woodfall is anger; the Deku king is trying to kill a young monkey who allegedly kidnapped his daughter.

Snowhead is bargaining; Darmani begs Link to bring him back to life.

Great Bay is depression; Mikau dies trying to save the eggs of his love interest Lulu, leaving her alone.

Ikana Valley is acceptance; the only thing Link has left to conquer is himself, facing his own grief at the loss of his friend. The friend who began the journey, Navi.

After receiving the Romani's Mask, if you protect Romani's Ranch from the invaders on the First Day, and help Cremia deliver the milk to Clock Town, you'll receive 1 of 3 rewards. Link can get either a Huge Rupee (worth 200 Rupees), some Chateau Romani, or a hug.

If Link receives the hug, Cremia will hold Link up close to herself and a message will appear saying "You did it! You helped Cremia!" "You feel all warm and fuzzy! inside! Sigh... You could get used to this!" The extra exclamation point after fuzzy was removed in later versions of the game.

After slashing a sign with your sword in Ocarina of Time, playing Zelda's Lullaby while near the sign will repair it. Once the song is finished, the solving a puzzle jingle plays and the sign magically repairs itself.

This same thing happens in Majora's Mask with playing the Song of Healing.

After slashing a sign with your sword, playing the Song of Healing while near the sign will repair it. Once the song is finished, the solving a puzzle jingle plays and the sign magically repairs itself.

This same thing happens in Ocarina of Time with playing Zelda's Lullaby.

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

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.