Notch tweeted a mysterious picture that, when brightened, revealed a player to be "flying" on a cloud. This was a scrapped idea for flying in creative mode, which was implemented in version 1.8.

Notch intended to include a "Sky Dimension", which would be the polar opposite of the Nether. It was to be included in the Beta 1.8 Adventure Update. Players would have been able to enter a world made up of floating formations once they slept in a bed. However, Notch delayed this new area until he could make the Nether more interesting. Eventually, the Sky Dimension was converted into the End, though the Sky Dimension was unintentionally able to be accessed in Beta 1.6 and 1.7.

Gears were a type of block that were available in Indev 0.31 which could be used in a similar way to redstone. They could only be placed on the side of blocks, and were never available in the release versions. In earlier builds players could hack the game to make them accessible, but the files were removed in later updates.

In the InDev version of the game, Notch may have planned to have furniture in the game, as found in the terrain.png inside the Minecraft Indev files. The idea was later abandoned.

Bedrock was originally known as "adminium" because it was only allowed to be broken and placed by admins.

When Beta 1.4 was released (April 1st, 2011), there was a small chance of every chunk spawning a block that is now called "Locked Chest" which, when right-clicked, displayed a menu saying "Steve Co. Supply Crate". This is a nod to Team Fortress 2's Mann Co. Supply Crates. Clicking the "Go to Store" button opened a browser window to the newly created Minecraft Store, which sold 12 items:
• Steve Co. Supply Crate Key ($3)
• Steve Co. Supply Crate Key 5-Pack ($18)
• Miner's Helmet ($21)
• Name Change ($99)
• Creeper Saddle ($42)
• Secret Griefer Identity ($155)
• Enlargement Pill ($2)
• Response From Support ($494)
• Three "Coming Soon" items (Priced at $75, $7, and $1499)
• "Regular Padlock" for $8.

Items could be "purchased" by clicking on them. Once the cart reaches $10,000 worth of items, a pop-up appears advising you to click cancel if you're prone to seizures. If you click OK, the screen starts flashing various colors.

Clicking the Checkout button caused a Velociraptor sound effect with an error in the "checkout" process. On April 2nd, a banner was added which floated the words "April Fools!" across the screen, accompanied by a midi instrumental of Rick Astley's "Never Gonna Give You Up".

The "Locked Chest" item was meant to be removed on the midnight of April 1st, but since the creator, Markus Persson, was sick, the item was removed on April 5th instead, the day Beta 1.4_01 was released.

According to Notch, The Enderman name is a reference to the creepypasta monster, "The Slenderman".

Endermen sounds are actually a person saying "Hi" and "What's up" played backwards and distorted.

A block known as Crying Obsidian was originally planned as a way for the player to set a new respawn point, but was abandoned and removed from the game after the release of beds.

The Iron Golems holding out roses to baby villagers is a reference to the ancient robots in the animated film Laputa: Castle in the Sky, as is the fact that the Golems are covered in vines.

According to former Mojang business and production director Daniel Kaplan, he came up with the original name for the mobile version of Minecraft, "Minecraft: Pocket Edition", a nod to the Game Boy Pocket, because he was a Nintendo fan.

According to Minecraft's creator Notch, the game's protagonist, Steve, and all other beings in the game are genderless. Animals were designed to be hermaphrodites (for instance, cows/bulls having both horns and udders) to reinforce this. Notch expressed regret in 2012 for refering the protagonist as "Steve" with masculine pronouns, prefering the "up-and-coming" they/them pronoun. He also joked that no gender existing in Minecraft meant that every animal and character in Minecraft is homosexual "because there's only one gender to choose from. Take THAT, homophobes!" It is unclear if Notch still stands by this, as he has since become an outspoken opponent of gay and transgender identities.