- In the original NES version, when Link is defeated, the screen flickers very fast in red, blue and green (similar to the banned Pokémon episode Dennô Senshi Porygon (1997)). To prevent seizures, blue and green were removed in the GameCube port to feature red in black instead. Later, the flickering was modified again for the Game Boy Advance port by slowing it down and change the colors to dark red and red.
- Several differences between this game's original Japanese version and its English-language release exist. Among the differences within the Japanese version are:
- The title logo is different and reads "THE LEGEND OF ZELDA 2" (in English) with a larger "RINKU NO BOUKEN" ("Adventure of Link", written in Japanese). Additionally, there is a "PRESS START" message under the logo.
- The title screen music has an additional sound layer and is of greater quality than the English version.
- The opening text scroll is different. It also contains quite a few spelling and grammatical errors, as well as a reference to "DISVALLEY", an erroneous transliteration of the Japanese version's name for Death Mountain, "DESUBAREE" ("Death Valley").
- The "REGISTER YOUR NAME" and "ELIMINATION MODE" selections on the file select menu are "NAMAE TOUROKU" ("Name Entry") and "KILL MODE", respectively.
- The file select menu's sound effects are different.
- Since this game was originally released on the Japan-only Famicom Disk System, which used a disk format that resembled a 3.5" floppy (as opposed to the regular Famicom and the English NES, which used cartridges), the game stops for a few seconds to read and load data in certain spots (such as when the player enters a town). When this occurs, a black screen with "W A I T" written in white letters appears.
- The water in the overworld map screen is animated.
- The palace in which players start the game has some smaller hallways instead of a consistently wide room like in the English version, and has no torches next to the sleeping Zelda.
- All palaces have white bricks, whereas the English version's palaces have differently colored bricks for each dungeon.
- The enemy sprites on the overworld map screen are different and somewhat resemble balloon-like objects. Minor enemy encounters are a light pink color, major enemy encounters are blue, and fairy encounters are red.
- Link has a slightly darker color scheme.
- The field battle music is different.
- Many in-game sound effects are different.
- Whenever Link levels up, the player may choose which stat (health, magic, or attack power) to increase; in the English version, the game chooses it for you. However, in the Japanese version, when the player gets a game over, the game resets all of the player's stats to the level of the least-developed stat the player had when the game ended. Thus, it is suggested that players of the Japanese version try to increase their stats uniformly.
- Experience point bonuses are different (and harder).
- Some palace layouts are different.
- There is no sound effect played when Link exits a battle.
- In the English version, when the player gets a game over, a red screen with a large silhouette of Ganon and the message "GAME OVER RETURN OF GANON" appears, and a sound effect of Ganon laughing is played. In the Japanese version, a plain black screen with "RETURN OF GANNON THE END" written in letters appears, accompanied by the sound effect of a boss roaring.
- In order to pick up extra lives, heart containers, etc. up, the player must stab them with Link's sword.
- The opening text scroll is slightly changed for the Gamecube "Zelda Collection" compilation disc, and the copyright text below it is different.
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