Every specific group of blocks purposefully formed in Minecraft based on coding is part of a natural structure.
The Overworld contains numerous generated structures, at a wide variety of scales.
Biomes dictate the shape and height of the world. At this stage, the ground is made entirely of stone, with water filling in any empty space below layer 63, with exception for structures.
Mountains are hills with extreme slopes and cliffs. Prior to the Adventure Update, these highly mountainous landforms were found in all type of biomes, but from the Adventure Update onwards are very rare outside the Extreme Hills biome. They were generated as part of the terrain generation algorithm. Mountains can sometimes have a cave spawned in the middle. On AMPLIFIED, mountains are extremely common in all biomes.
A picture of an extreme hills biome
 Floating "island"
Floating "islands" are structures that float in midair that are not connected to the ground, the sea, hills or cliffs. Floating "islands" are normally just random pieces of floating dirt and stone found near cliffs, but on rare occasions they can be large, floating structures that even have springs and trees on them. Floating Islands are most frequently found in the Extreme Hills, Ice Plains, Ice Mountains and Mushroom Island biomes, but can be found anywhere. In Multiplayer, they can be a useful place to put your base because they can be hard to reach. Floating Islands are extremely easy to find on an amplified world.
Hills are randomly generated pieces of land in the map. Like stairs, hills are always traverse-able to their lowest point by virtue of the algorithm which generates them; there is almost always a place on each level from where the next level can be accessed, meaning that the player can climb a hill one level at a time until they reach the top. Cases where this is not true are rare.
Beaches usually generate next to oceans and cover all nearby shorelines. They come in three varieties: sand beach, gravel beach, and stone beach. Sandstone is located below sand in sand beaches. Gravel beaches had no such border and thus pose dangers like falling into caverns located right underneath them. Stone beaches have cliffs near the ocean.
 Surface layer
The uppermost layers of the terrain are converted to a biome-dependent material: usually grass and dirt, or sand in deserts and beaches. Podzol is found in Mega Taiga, and red sand is found in the Mesa biome. Sandstone is generated under sand.
Occasionally, instead of being converted to dirt or sand, the top layer is stripped away, leaving a 'Basin' of bare stone. There is a common misconception in the community that these are errors; however, they are an intended feature (however, some confirmed bugs create basin-like effects as well). They bear some resemblance to a geological 'shield' (an area of tectonically stable rock that has been exposed to prolonged erosion due to its very old age; it is distinct from the geological term "basin"). They seem to be more common in Forest or Plains, and are sometimes seen filled with water. Sometimes, common minerals can be found on the surface such as coal and iron ore.
 Water Bodies
Oceans/Seas are huge bodies of water with every single water tile being a source block. The ground can rise high enough to produce small, relatively barren islands. Prior to the Adventure Update, oceans were generated as part of the terrain generation algorithm, but since then, they are part of the Ocean biome.
A picture of an Ocean biome
Rivers are long "strands" of water that cut through or separate biomes. They have no current. Rivers have also been known to be a reliable source of clay. In hilly or mountainous areas, the ground can rise above layer 62, producing a dry riverbed.
The first image of a river released by Notch, with a Huge Mushroom next to it. (Note: Huge Mushrooms don't spawn naturally outside of Mushroom biomes and Roofed Forests.)
 Large structures
Caverns are caves and tunnels that are automatically generated under the ground in various places. Caverns are composed mainly of stone, and contain large amounts of ores. In caverns underneath deserts or beaches, you can see sandstone stalactites.
A dark cave with a zombie
Ravines are tall, long cracks of air, usually measuring around 30 to 50 blocks in height, making them quite dangerous if one should fall down. However, they are narrow, usually no more than 5 blocks wide. Ravines can have small ledges along the top, which can be traversed with relative ease. Ravines can be found at any level and also sometimes appear on the world surface, forming canyons—a serious hazard when wandering around the countryside, as they may not be obvious until one is right at the edge... or over it. Such canyons do, from time to time, appear underwater where safe entry is possible. They can go very deep underground, sometimes spawning slimes or exposing diamond ore. If they reach deep enough, they may also be floored by the lava lakes at level 11, meaning you don't need to worry about mobs spawning as much - you've got an even worse hazard underneath. In the Amplified world type, ravines can reach from surface level to bedrock. Ravines can also be found in oceans or rivers having a waterfall from the river/ocean falling into them.
Ravines can connect to caves, dungeons, abandoned mines, and any other generated structures. Due to the large surface area of their walls, ravines often have water and/or lava flowing down them (from springs in the walls, underground lakes, or even openings to the sea). The player can also add his own waterfall(s) from the edge in order to descend more safely but should be aware of potential threats such as lava flow and hostile mobs.
 Abandoned mine shaft
Abandoned Mine Shafts are structures generated underground which consist of branching mining tunnels with wooden supports and broken rails passing through it. This is also the only place in Minecraft where venomous Cave Spiders can be found. It is easy to get lost in the labyrinth if torches or other reminder blocks are not placed. Open areas generate with bridges instead of leaving floating platforms. They contain minecarts with chests that may have rare items such as diamonds and horse armor. They may also contain iron ingots, coal, pickaxes, and other useful items. They are likely to expose veins of coal, iron, lapis lazuli, gold ore, and rarely, emerald and diamond ore.
Strongholds are structures that contain multiple rooms, doors and other aspects (some of these rooms include libraries, fountain rooms, dungeon-like rooms, etc.). stone brick, mossy stone brick, cracked stone brick, doors, iron bars, Monster Eggs and stone slabs are the materials that make up the strongholds. They also contain silverfish, which one should be careful of when digging around in strongholds. Portals to The End are found in specific rooms in strongholds. Chests may be found containing items such as books, Redstone, Ender pearls, apples, bread, compasses, iron tools/armor, and diamonds. Strongholds can be found by right clicking an Eye of Ender, which will be thrown into the air and point the direction where the End Portal is, showing the way to the Stronghold.
 Small structures
The quantity of most of these features (aside from lakes, mineral veins, and springs) are biome-dependent; not all of them can be found in every biome. (Example: A small jungle maze/trap made out of cobblestone, redstone, dispensers, arrows, wooden pressure plates and a chest that usually will contain an iron tool/weapon)
Lakes are small bodies of a liquid. Water lakes can now be generated above sea level or inside caverns, and are small bodies of water surrounded simply by dirt or sand. When in a winter biome, these small lakes are never initially frozen but can turn to ice. The lakes can also be composed of lava; however, lakes of lava are more rare. Lava lakes found at the surface may be surrounded by gravel, sand, stone, and coal ore. Both types of Lake generate with a small air pocket above them, which may result in floating sand, floating snow cover or even the top 2/3rds of trees above the lake. Lava Lakes may cause trees to burn this way.
Dungeons are small, mostly underground, one-room spaces bordered by mossy cobblestone and cobblestone, and typically contain chests with rare items, and a hostile Monster Spawner in the center, which guards the chests. The monster spawner can spawn either zombies, skeletons, or spiders (the last will include occasional spider jockey). Occasionally a player may find that the mob spawner is covered with gravel and will be harder to reach, yet the mobs can still spawn with the gravel around it. Usually, placing a torch on the spawner will prevent mobs from spawning. The chests may contain rare valuables, such as music discs, enchanted books, saddles, horse armor, and golden apples. Rarely, there may be two dungeons generated right next to each other, this can make two dungeons in only about one space. There have also been reports of three or more dungeons in very close proximity to each other. There is a small chance of not getting a chest. Dungeons generated in a desert can sometimes be visible from the surface due to the sand falling down.
 Mineral vein
A mineral vein is a natural deposit of ores. Players can come across these veins in caverns or anywhere where there is natural stone. Underground deposits of dirt and gravel are generated in this step, followed by the more precious ores: coal, iron, gold, Redstone, diamond, emerald (in extreme hill biomes) and lapis lazuli. They can only form in Stone, and do not replace each other or any other block.
Trees are common structures created both during world generation and by players (grown from saplings). They are made of wood and leaves. Tree sizes range from small trees that can be fully harvested from ground level, to large trees that may require several minutes to harvest.
 Huge Mushroom
Huge Mushrooms are structures that only naturally occur in mushroom island biomes and roofed forest biomes. They are composed of mushroom stalks and either red or brown colored blocks for the cap. They can be grown outside Mushroom Islands by fertilizing red or brown mushroom with bone meal, or can be generated with mycelium. Huge Mushrooms can also be found anywhere in AMPLIFIED, but each will spawn with groups of 1-5 mushrooms per group.
Springs are randomly generated blocks of either lava or water that act as a source of their respective material. While both can be found on the vertical side of stone blocks above the surface, lava springs are more often found underground beneath layer 32 in caverns. Both of these sources can be collected and moved via the use of buckets. Springs can only be found in versions from Infdev onward, as fluids behaved differently in older versions.
 Desert well
These well-like structures built of sandstone blocks and slabs generate only in the desert biome. Although assumed to be wells, their exact purpose and function is yet to be known. A proposed reason would be for filling buckets with water, since the middle water spring is infinite. Also, it is possible for a well to spawn over a stronghold or an abandoned mineshaft. They have a 1/1000 chance to be generated in any desert chunk, which makes them a rare sight. It is possible for a well to generate around a cactus. The well structure can also spawn even with the "Generate Structures" setting disabled. As of 13w17a (snapshot of 1.6.1) water lakes no longer generate within deserts, thus making desert wells (and desert village farms and wells) the only "natural" source of water in desert biomes.
 Moss stone boulder
These structures are meant to represent boulders, made entirely of Moss Stone. The formation of these structures vary possibly infinitely. They can be found dotted around areas of the Mega Taiga biome. Due to the wide variety in shape they often appear to just be a patch of moss stone on the ground rather than a boulder. They provide an easier source of Moss Stone than do Dungeons and Jungle Temples. However, as with Ice Spikes, Moss stone boulders are quite rare, due to the Mega Taiga biome's rarity. They are rarely big enough to live in.
 Ice spike
Ice spikes are tall spires made of Packed Ice. The spikes can only be found in the Ice Plains Spikes. There are two variants of ice spikes: one is short and thick, and the other is extremely tall and thin.
Buildings are naturally generating structures that form above ground. They can contain valuable treasure, but traps and puzzles as well.
Villages are generated in Desert, Plains and Savanna biomes and are a site for villagers, who can be traded with. They are composed of a random selection of various buildings and farms. There is always exactly one well, other buildings can be any of several different houses, single or double farms, blacksmith's shop, library, butcher's shop, or church. Villages are built with different materials depending on their biome: Oak wood and cobblestone for Plains villages, sandstone for Desert villages. Villages RARELY generate partly submerged in water, although this is more prominent in the Console editions. The Villagers move about in the area around the village, retreating indoors at night and during storms. Villagers vary in their professions (indicated by their clothing), which affects the items they will trade.
 Desert temple
Desert temples, also known as pyramids, are found in deserts. They mainly consist of sandstone and wool. In the middle of the temple is a block of blue wool, which if destroyed, reveals a deep, hidden chamber underneath, where players can find 4 chests, which can contain valuable loot, and a stone pressure plate trap connected to a 3x3 grid of TNT. Treasures found in the chests include emeralds, diamonds, iron ingots, gold ingots, rotten flesh and bones. While rotten flesh, bones and gold ingots are found frequently, other treasures are not as common.
 Jungle temple
Jungle temples are found in jungles, and mainly consist of cobblestone and mossy cobblestone. There are three floors, the bottom floor containing a chest and a puzzle. The chest is found through a corridor which contains hidden tripwires that triggers a dispenser to shoot arrows at the player. The player must carefully navigate through the corridor while triggering the tripwires. The puzzle is located at the opposite of the corridor and consists of three levers that must be pulled in the correct order to open a secret door which reveals another chest. The solution to the puzzle can be found here. While both chests can contain rare loot, the puzzle chest usually contains the more valuable ones, such as diamonds and emeralds.
 Witch hut
Witch Huts generate in swamp biomes. Witches spawn inside of them. The huts consist of spruce wood planks and oak wood. Spruce wood stairs make the roof borders, 2 fences decorate the entrance, one fence makes the front window bars, and one fence makes the back window bars. Inside is a crafting table and an empty cauldron. Potted mushrooms decorate the windowsills and it is possible, but rare, for additional, unpotted mushrooms to generate inside. There are no chests or any other loot inside. Strangely, witch hut ceilings are just high enough for the witches to fit inside, but their hats protrude into the ceiling, making the animation look broken. There is no valid way a witch can get back up into a hut if it falls out of one (other than player intervention or the extremely rare case of one or more endermen building a staircase by accident). The hut's design seems to be based on the hut of Baba Yaga, a witch from Slavic folklore who lived in a hut that walked around on giant chicken legs.
 Ocean monument
Ocean monuments are upcoming structures in 1.8 that spawn in deep oceans. They spawn in the shape of a pyramid with many rooms. They are composed of Prismarine, Sea Lanterns and Prismarine Bricks. The only valuables found here are 8 gold blocks encased in Dark Prismarine and a random assortment of Sponges. Guardians and Elder Guardians spawn here.
The Nether, though equally vast, contains far fewer types of generated structures than the Overworld.
 Lava sea
Lava seas are found at and below level 30 in the Nether. They make a large portion of the Nether, and are extremely common. They can stretch for hundreds, if not thousands, of meters in any direction, and are usually bordered by Netherrack (or more rarely soul sand). Even on far render distance, the player is rarely able to see the other side of the seas due to their vastness.
A lava sea with Ghasts taking a dip in it
 Nether fortress
Nether fortresses are very large complexes made mainly of nether bricks (with added nether brick fences and stairs to be found). Due to this, it is very easy to get lost in them and it may be difficult to navigate back to portals. Nether fortresses can often tunnel through Netherrack. and the inside of the tunnels will be cleared of Netherrack by the terrain generator. Blaze spawners and nether wart farms are only found in Nether Fortresses. Aside from the spawners, Blazes can spawn anywhere in the fortresses, and there are also not only Zombie Pigmen, but Wither Skeletons as well. Nether Fortresses have some chests. The chests with loot are usually generated in corners.
A nether fortress generated in the Nether
 Glowstone cluster
Glowstone clusters are typically veins of glowstone that can be among the hardest natural materials to harvest that don't require digging. They form in coral-like structures on the underside of hanging Netherrack, so they are often found on the ceilings of the Nether, where they provide light along with the ever present lava. Luckily, there are places where the ceiling is very low, and veins there can usually be mined without undue risk.
 Other things
There are areas of soul sand and gravel around layer 64, and as of the 1.5 update, there are Nether Quartz ore veins and "hidden lava", which is a single block of lava in random places not visible without digging.
The End is the most barren dimension, with only four types of significant structures.
 The island
Most of the End is a large, asteroid-like island composed entirely of End Stone, floating in an endless void.
 Obsidian pillar
Obsidian pillars, or obsidian towers, are tall, tower-like structures that generate in The End. No part of them are in the ground; there is no obsidian below the lowest block of obsidian that the player can see without digging. Ender Crystals will spawn on top of each one to heal the Ender Dragon.
On the Console Edition, the Pillars are generated in a Circle around the fountain. Two of the Ender Crystals are surrounded in iron bars, which must be destroyed before the Crystal can be taken out.
Obsidian pillars can be hollow.
 Obsidian platform
The obsidian platform is a 5 by 5 square of obsidian that the player spawns once they enter The End. (Note that if the Obsidian is destroyed, or if a block is placed on top of it, when the player returns to The End, the obsidian will be restored and any blocks on top of it will despawn.) Obsidian platforms mostly spawn far away from the island, making it tough to get there.
- Sometimes the platform spawns inside a case of Endstone. It will remove enough Endstone so that the player can walk around.
- Occasionally the platform will spawn in midair.
- Very rarely, the platform will spawn on an obsidian pillar and have an Ender crystal on it.
 End fountain
Sky (The End)
Yes, when the Ender Dragon is defeated.
The exit end portal, in the shape of a fountain is found once the Ender Dragon is defeated, giving the player a way back to the overworld. This fountain is also the foundation of the Ender Dragon Egg. After entering the fountain, the Minecraft credits come on the screen, implying that you have "beaten the game" (despite the fact that the game never ends). You can skip these credits by pressing Esc. After the credits have finished (or after you skipped them), the player returns to the last bed they slept in (or their original spawn spot if the bed was obstructed). The fountain is also made of bedrock, making it indestructible.
On the Xbox 360 Edition, the Fountain is generated in between the Pillars, and already exists before the Enderdragon is killed. The Enderdragon will also fly above the fountain when the player approaches it, and spew Ender Acid. However, to truly defeat the Enderdragon and activate the fountain, you must land the finishing blow on the Enderdragon while it is above the fountain.
|1.8||Sand and gravel beaches removed due to the changes in the terrain generation algorithm.|
|1.8pre1||Added Abandoned Mine Shafts.|
|1.0.0||Added the End and End-related generated structures, including the End island, the obsidian platform, the obsidian towers and the end fountain.|
|1.1||12w01a||Sand beaches have made a return, but the way they look and generate are not the same as before.|
|12w07a||The generation of beaches has been greatly improved.|
|1.2.1||?||Previously, it was possible for lava lakes to spawn 1 block above bedrock, removing the bedrock and replacing it with stone (which on survival could allow access to the void).|
|12w04a||Desert wells were added.|
|1.3.1||12w21a||Added Desert temples.|
|1.4.2||12w40a||Add witch huts.|
|1.6.1||13w17a||Water oases no longer generate in deserts.|
|1.7.2||?||Mountains are more common in other biomes.|
|13w36a||Gravel beaches have been returned to the terrain.|
|The desert oases appear in the Desert M biome.|
|Moss stone boulders were added.|
|1.8||14w25a||Added Ocean Monuments.|
|Pocket Edition Alpha|
|0.9.0||build 1||Added villages, caves, lava pools, rivers, abandoned mine shafts, huge mushrooms, moss stone boulders, strongholds, ice patches, ice spikes, dungeons and desert wells.|
|TU5||Added villages, abandoned mine shafts, strongholds and ravines.|
|TU12||Desert wells were added.|
In previous versions when snow cover wasn't solid a Lava Lake leaving floating snow cover above it could be a deadly trap in the first 2 minutes after being generated (longer than that and the snow melts).