Inside the Deku Tree

The Great Deku Tree is the giant guardian of the Kokiri Forest. When it contracts a mysterious disease, Link must venture inside to destroy the tree's scourge and to break Ganondorf's curse, making it the game's first dungeon. It is infested with parasitic creatures, the main one being Queen Gohma. This dungeon contains the Fairy Slingshot. To enter the dungeon, Link must show Mido, who is blocking the way, the Deku Shield and Kokiri Sword.

The Great Deku Tree contains five floors, and most of the puzzles require Link to kill any enemy or destroy thick webs through the use of fire. Some smaller rooms can only be accessed later in the game. The final puzzle appears in the form of three Deku Scrubs which must be defeated in the correct order (second in line, third in line, and first in line) to face the boss, Gohma. There is no one mini-boss in this dungeon, although there are two individual deku scrubs in the dungeon, as well as the aforementioned group at the end.

Strangely, the sealed room in the basement of the dungeon containing the final Gold Skulltula does not appear on the map until it is visited, even after Link collects both the Dungeon Map and Compass. This is the only time in the game this happens, as the dungeon maps otherwise always show the entire dungeon.

Master Quest
In the Master Quest version of the game, besides the obvious change in the puzzles and Gold Skulltula locations, Gohma Larvae now appear all over the dungeon, along with Keese and some Big Deku Babas. There is a Business Scrub that sells a Deku Shield, and the Deku Scrub that reveals the code for accessing the boss's room is missing and has been replaced for a Mad Scrub. The slingshot and compass locations have been switched.

Minor Enemies and Traps

 * Deku Babas
 * Deku Scrubs
 * Skulltulas
 * Skullwalltulas
 * Gold Skulltulas
 * Gohma Larvae

Trivia

 * This dungeon can be entered as an adult by using a Mega Jump glitch while on top of the Twins' House. It can be fully completed as an adult, provided that the player has obtained the fire arrows or din's fire. However, the bow is unable to stun Gohma for some reason. Instead, the player must use deku nuts to stun her.
 * This dungeon is one of two that require the player to return at a later point if they wish to collect all of the gold skulltula tokens, the other dungeon being Dodongo's Cavern.
 * This dungeon and Dodongo's Cavern are the only ones in the game without a dungeon music theme. Instead, the secret grotto theme is heard in the Deku Tree dungeon, whereas the alternative underground theme (correspondent in Thieves' Hideout and Royal Family's Tomb) is heard in the Dodongo's Cavern dungeon.