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.

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

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

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.

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

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.

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.

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.

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.

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.

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.

Some of the paintings in the game are maps from the game Counter-Strike.

If you name a Mob creature "Dinnerbone" or "Grumm" (using a name tag) the creature will flip upside-down. This is an Easter egg put into the game by the developers, Nathan "Dinnerbone" Adams and Erik "Grum" Broes.

There are four unused paintings in the pocket edition. Information on who drew these paintings, and their purpose, is unknown.

In the TU12 world of the Xbox 360 version of the game, it's possible to find a pyramid. Inside is a tower of 4 gold blocks placed on an obsidian block. This is a reference to Rooster Teeth's series "Let's Play", where each week 7 guys play different challenges in Minecraft: Xbox 360 Edition to win a golden tower they call the "Tower of Pimps".

The texture of the Zombie Pigman has "thx xaphobia" written on it as a credit by Notch to the skin's original creator, XaPhobia.

If you delete the file 'splash.txt' without deleting the META-INF folder, the splash text on the title screen will say 'missingno'. This is a reference to the infamous Glitch Pokémon, MissingNo.

The achievement "Adventuring Time" is a reference to the Cartoon Network show "Adventure Time".

There's a chance that the splash text on the title screen will read "12345 is a bad password". This could be a possible reference to a scene in the 1987 film Spaceballs.

One of the splash texts in Minecraft is "Consummate V's!" This is a reference to the Homestar Runner "Strong Bad Emails" episode, "Dragon", in which Strong Bad explains how to draw Trogdor. This includes drawing "consummate 'V's" for teeth.