Five humanoid mobs which were available in the Indev version were later removed. However, they can be found in the files of earlier versions of the game. The mobs were Beast Boy which resembles the DC comics character of the same name, Black Steve, humans which resemble the default player's character (later renamed 'Monsters'), Rana who is a little girl with a frog hat, and a different human also named Steve.

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.

The Leather chain armor is a sprite from Indev (an older test version of Minecraft's Survival mode) 0.31's items.png armor. It never made it to the release versions.

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.

Notch would always drop a red apple when killed in earlier versions of Minecraft.

In Minecraft Pocket Edition, there's an unused camera. If hacked into the player's inventory, it can be used to take pictures.

Villagers were inspired by the shop keepers in Dungeon Master 2.

Lightning does not have an image file associated with it. It is coded directly into the game engine.

The Snow Golems don't actually have pumpkin heads. They simply wear them as a helmet and their actual faces can be seen by standing in very close proximity to them so that you see through the pumpkin. Shears can be used to remove the pumpkin and cause one to drop it revealing its face, although the pumpkin cannot be put back on the Snow Golem.

There's a very rare chance that the "C" and "E" in the Minecraft logo will switch and instead show "Minceraft".

Emeralds were originally supposed to be rubies, but they were changed to emeralds due to Dinnerbone (Nathan Adams) being color-blind, making him not able to easily tell the difference between redstone ore and ruby ore.

The game was partly inspired by an earlier game by Notch called RubyDung. It was more of a Base-Building type game, like Dwarf Fortress. The old Cobblestone texture came from this game.