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.

One achievement in Minecraft is called "The Lie", which includes making a cake. This is a nod to Portal's famous meme, "The Cake Is A Lie". Also, the achievement for entering the nether in the PC version is called "We Need To Go Deeper", which is a reference of the multi-layered dream based plot of "Inception".

When Soul Sand is directly placed over an ice block, its slow effect is greatly increased, affecting both mobs and players.

"Herobrine Removed" has been added to a number changelogs. Herobrine is a character from a Minecraft "creepypasta" who looks exactly like the player, but has white eyes. It is said that Herobrine is Notch's dead brother, although Notch said himself that he does not have a dead brother. Herobrine never appeared in the game, and it's likely that this line being added to the changelogs is just a joke with the community.

Steve once had a beard, but it was removed in the beta update.

The in-game NPC Villagers, often referred to as Testificates, were originally planned to be Pigmen, much like the Nether mobs. (Except not undead.) They would have the standard player model like Zombies and Zombie Pigmen, but with a Pig's skin. The second Skin Pack for the Xbox 360 version contains a Pigman skin as a slight nod to this.

Originally, zombies used to drop feathers when killed. This was the result of Notch, the developer of Minecraft at the time, not knowing what zombies should drop.

The Creepers were based on a failed model of a pig. The length and the height of the pig model were accidentally inverted, resulting in a tall mid section with small legs.

When enchanting an item, the strange symbols used to describe the kind of enchantment is actually a direct usage of the Standard Galactic Alphabet from the Commander Keen series for DOS.

The texts respectively read "Well Played Internets You Are Good", "These Names Will Be Random And Confusing" and "Each Spell Costs Experience Levels" describing the function of the enchantment table.

Diamonds were originally called Emeralds. Because of the light blue color they had, Notch decided to change the name to diamonds. In the code of Minecraft, Diamonds were still referred to as emeralds until 1.3, which introduced the current item known as Emeralds.

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.

Minecraft was originally called "Cave Game".