Early builds of Pokémon Gold and Silver indicate that Celebi was originally designed after Kokopelli, a trickster figure, mythical flautist, and fertility deity worshiped by certain indigenous tribes in the American southwest (most prominently the Hopi and Anasazi). This is most apparent in a leaked build from May 6, 1998, in which Celebi's sprite is nearly identical to modern depictions of Kokopelli, with the only major deviation being the addition of eyes. A later design is present in the data for the Spaceworld 1999 demo, bearing a closer resemblance to Celebi's finalized sprite but retaining the Kokopelli motif.

Within the games' data is a scrapped map for a dense, maze-like forest leading up to Mt. Silver. Since the mountain is inspired by Mt. Fuji, the maze is likely derived from Aokigahara, a forest at the base of Mt. Fuji that is famous for its density and natural soundproofing. Because Aokigahara is also notorious for its popularity as a suicide site, it's likely that the maze was removed in favor of a shorter, more conventional route to avoid stoking controversy from Japanese audiences.

Because of an oversight, the Fast Ball, which is supposed to work better on Pokémon that have a proclivity to flee, only works as it should on Magnemite, Grimer, and Tangela. This is because the Ball is supposed to look for three categories of Pokémon: ones with a 10% flee rate, ones with a 50% flee rate, and ones with 100% flee rate. However, for some reason the ball only chooses the first three Pokémon in the first category (10% flee rate) when it applies its catch-rate modifier.

If you get the Dragon Fang through trading or by hacking it into the game rather than getting it from the shrine within Dragon's Den, Clair will call you out for cheating and will not give you the Rising Badge until you get the Dragon Fang yourself:

According to Ken Sugimori, the Pokémon that appeared in the front page of the 1997 edition of MicroGroup Game Review showcasing Pokect Monsters 2 were not supposed to appear in the game at all. While some were never to be seen, Tyranitar ended up being used. This explains why Tyranitar wasn't in the leaked 1997 prototype ROM.

Originally, the region of Johto was based on the entirety of Japan, rather than just the Kansai region, with towns and dungeons based on areas within the country, such as Hokkaido (called North in the Spaceworld 97 demo), Osaka (which was called West and likely became Goldenrod City) and Mt. Fuji (which likely became Mt. Silver). Due to this, Kanto, which was based on the region in Japan of the same name, was compressed into a single map, with Blue as the Gym Leader.

Evolved and pre-evolved forms for Tangela, Qwilfish, Goldeen, Vulpix, Paras, Ditto, Doduo, Meowth, Mr. Mime, Growlithe, Lickitung, an alternate evolution for Weepinbell, Farfetch'd, Pinsir and a Grass type evolution for Eevee, were implemented in the demo featured at Nintendo's Spaceworld 97 show. All of these evolutions were cut from the final product.

Gold and Silver originally had a completely different looking starter trio. They were Happa (grass), Kurusu (water) and Honōguma (fire). The grass starter's design remained somewhat similar in the final release, becoming Chikorita.

In Generation II, Cerulean and Fuchsia City didn't use their music from Generation I, and shared themes with Celadon City and Viridian City, respectively. However, when remade, Cerulean and Fuchsia were given their Generation I theme again, but because they didn't have this theme in Generation II, when using the GB Sounds, an original Generation II-styled remix was used.

The song for the Bicycle theme is actually a sped up version of the Goldenrod City theme with different instruments.

In this generation, Smeargle's normal and shiny colors are reversed - its shiny being green instead of red. Pokemon Stadium 2, Pokemon Colosseum, and Pokemon XD: Gale of Darkness also have this issue. Pokemon Colosseum and Pokemon XD: Gale of Darkness have this issue because they reuse models from Pokemon Stadium 2.

Due to a glitch in the game's code, burn, paralysis and poison statuses don't affect the catch rate of a Pokemon.

Because of a glitch in the game, Moon Balls don't work as they were planned to. Moon Balls were supposed to increase the catch rate (x4) when trying to catch a Pokémon that evolves using a Moon Stone. Instead, they were programmed to increase the catch rate when you try to catch a Pokémon that uses a Burn Heal (an item not related to evolution at all) to evolve.

There's an unused script that triggers a battle with a level 40 Entei upon contact. It might be that early in development, the Legendary dogs would have been battled normally like the legendary birds in Gen 1 instead of searching for them in the grass.

At one stage in development, it was possible to name the player's mother.

When the NPC Trainer Firebreather Dick at the Burned Tower is defeated, his overworld sprite pallete changes to black and white until the player exits and reenters the area.

The clouds on Gold's title screen and the sea floor on Silver's title screen are just recolors of the same image.

Lance's Aerodactyl knows Rock Slide. This is odd as Aerodactyl could not learn Rock Slide until Ruby and Sapphire.

The map of the Pokémon Laboratory on Cinnabar Island can be found complete in the data for Gold and Silver. This could suggest that there were once plans to include the laboratory in the game.

Most of Pokemon Gold and Silver's music was created on an Amiga computer, converted to MIDI, and then reconverted to the game's music format. Some songs, though, like the Unown radio music, were created by hand directly in the GSC music format.