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A mini-dungeon does not consist of a whole dungeon but contains some elements of a dungeon. Hidden Holes are not considered mini-dungeons. Mini-dungeons usually must be completed as part of the storyline. Hidden dungeons do not count as mini-dungeons because they are not necessary to complete the game.
- Hyrule Castle holds the Boomerang, but the "boss" is a normal enemy and does not have boss music, and the Heart Container is actually located in the Sanctuary. It is located in the center of the map.
- Hyrule Castle Tower has no item and no Heart Container, but it has a boss, Agahnim. It is located directly on top of Hyrule Castle.
- Kanalet Castle has no item and no Heart Container, but in and around the castle can be found the Golden Leaves that Richard requires. It is located to the north of Martha's Bay.
- Face Key must be retrieved from the Ancient Ruins to enter Face Shrine. The Ancient Ruins has no heart container but has a Armos Knight as a miniboss before you receive the key.
- The Ice Cavern holds the Iron Boots that can be obtained after fighting the White Wolfos. The "Serenade of Water" is also learned here. It is located in Zora's Fountain, but is only accessible when Link is an adult, when the entire Zora region is frozen. It is also where Link can obtain Blue Fire which he can store in a Bottle and is the only place besides the Inside Ganon's Castle where he can obtain it for free.
- The Bottom of the Well holds the Lens of Truth, and the mini boss Dead Hand, but no Heart Containers or Pieces of Hearts can be found. The well is located in the heart of Kakariko Village and is only accessible when Link is a child and after he has drained the Well by playing the Song of Storms in Kakariko Windmill.
- The Gerudo's Fortress contains several Gerudo that act as mini-bosses and defeating all the Gerudo Thieves and freeing the Carpenters earns Link the Gerudo Membership Card from Aveil, which is required for Link to progress to the Haunted Wasteland, Desert Colossus, and Spirit Temple.
- The Gerudo's Training Ground holds the Ice Arrow in an optional mini-dungeon. It is worth ten rupees to go inside.
- The two spider houses are in different locations. The Swamp Spider House holds the Mask of Truth and the Oceanside Spider House holds the Wallet upgrade.
- The Deku Palace has no boss, but it is where Link first obtains Magic Beans and the Song of Awakening is learned here after making it passed Deku Palace Guards and Mad Scrubs.
- The Pirates' Fortress holds the Hookshot when using an arrow to destroy the Beehive scaring away Aveil and the other Gerudo inside.
- Beneath the Well contains the Mirror Shield that can be only be reached by giving items to Gibdos which can be spoken to while wearing the Gibdo Mask.
- The Ancient Castle of Ikana has no item, but the "Elegy of Emptiness" is learned here after fighting Igos' Servants and the Igos du Ikana.
- The Great Moblin's Keep has no item and no Heart Container, but it has a boss, the Great Moblin. It is located on Rolling Ridge in the present age.
- Ambi's Palace has no item or Heart Container, but it has a boss, Possessed Nayru. It is located to the north of Lynna Village in the past.
- The Maku Path has no item, no Heart Container and no boss, but passing through the dungeon is required to reach the Maku Tree's grove.
- The Moblin's Keep has no item or Heart Container, but the Great Moblin is fought there. Interestingly, upon the defeat of the Great Moblin and the destruction of the keep, Link finds a Piece of Heart in the ruins. The Moblin's Keep is located in the Great Moblin's Realm, just west of Sunken City.
- The Savage Labyrinth has no item, Heart Container, or boss, and is found on Outset Island. It has fifty floors, each with all various enemies, increasing with difficulty as Link descends. At the thirtieth floor, there will be a Triforce Chart, necessary to find a piece of the Triforce of Courage. After obtaining the Mirror Shield, Link can travel down further to the final twenty levels. At the absolute end of the Savage Labyrinth is a Piece of Heart.
- Also Ice Ring Isle and Fire Mountain are also considered mini-dungeons. This is due to them not having a boss, nor many rooms, but containing the Iron Boots and the Power Bracelets respectively, both important items necessary to complete the game. There are also time limits to complete them, creating a difficulty setting.
- The Royal Crypt has no item, heart container, or boss. However, it is filled with traps and enemies, and it is necessary to complete the game. It is located in the Royal Valley.
- The Cave of Ordeals has no item, Heart Container, or boss. It has fifty floors, each with several enemies that get harder as Link descends, similar to the Savage Labyrinth. Every ten floors the Great Fairy appears and releases fairies at each Spirit's Spring. The prize at the end is Great Fairy's Tears, a cure-all substance. The Tears can then be found at any of the fairy springs around Hyrule. It is located in the Gerudo Desert.
- In Twilight Princess HD, there is a special mini-dungeon called the Cave of Shadows which can only be accessed via the Wolf Link Amiibo. The mini-dungeon is unique in that Link is stuck in his Wolf Link form while inside the dungeon itself. Completing it grants Link a new Wallet upgrade (if he has the Giant's Wallet he will receive the Colossal Wallet which allows him to carry 9,999 Rupees).
- The Waterfall Cave has no item, Heart Container, or boss. However it is filled with enemies and Link must pass through it in order to free his Crimson Loftwing. Link is also required to obtain the Practice Sword in order to access it. In many ways it is a mini-dungeon that acts as a tutorial for combat and dungeon-based exploration.
- The Pirate Stronghold has no item, Heart Container, or boss. It has a central puzzle involving a Timeshift Orb. Link must carry the orb throughout the entire dungeon in order to solve its puzzles. When Link finishes the mini-dungeon, he gains the ability to dowse for the Sandship.
- The Yiga Clan Hideout has items and a boss. Link must used stealth strategy or confront enemies, Yiga Footsoldiers and Yiga Blademasters. The boss Master Kohga is battled upon reaching the end of the hideout and a Thunder Helm will be obtained as a reward.
- There are three mazed mini-dungeons consisting of labyrinths housing a Shrine at their center. They are invaded by several enemies but not bosses or mini-bosses, and are located at the three corners of Hyrule, the Lomei Labyrinth Island in the Akkala Sea northwest region, the North Lomei Labyrinth in the Tabantha Tundra northeast region, and the South Lomei Labyrinth in the Gerudo Highlands southwest region of Hyrule.
- The Trial of the Sword from "EX Trial of the Sword", despite acting as a DLC Shrine, resembles mini-dungeons similar to the Cave of Shadows, Cave of Ordeals, and Savage Labyrinth. It contains rooms full of multiple enemies that get progressively harder. At the end of this trial, the Master Sword's glowing "true" power state is unlocked permanently.