Both early artwork of Bellossom and its Gold and Silver artwork show that it was originally a similar color to its other evolutionary relatives. A possible explanation for the change to its current color scheme would be the intention to avoid another racial controversy, as the original Bellossom design appears similar to traditional polynesian dress. However, this is unlikely to be the case.

The unused Bird type from the Generation I games remains in the Gold & Silver's code. This is presumed to be a carryover from the Generation I games' engine, as Pokémon Gold & Silver were developed on an upgraded version of it.

In a MicroGroup Game Review it shows unknown female and male trainers who never appeared in the final game. It also shows 2 unnamed Pokemon and an early version of Tyrannitar.

In Gold, Silver, & Crystal, the shiny Charizard sprite was a light shade of purple with green-blue wings. Starting with generation 3 though, it was changed to black with red wings for unknown reasons.

Pokemon Gold & Silver started out as Pocket Monsters 2. It was planned to come out in 1997, but due to delays and other issues the name was dropped. One year later the game was re-announced as Pocket Monsters: Gold & Silver.

When Red is encountered at the summit of Mt. Silver, he has no dialogue, merely repeating sets of ellipses before beginning the battle. This is a reference to his silent role in Generation I, as he only answered yes or no questions. This trait carried forward to future generations, including the HeartGold and SoulSilver remakes.

In the Ruins of Alph, the PokéGear will lose signal. Accessing the Radio function in this area will, instead of giving you the normal radio songs, give you a haunting sound, which is generally accepted to be the cries of the Unown.

In the code for Gold & Silver, there are various pieces of unused dialogue that refer to an item called "Sweet Honey." This implies that the honey mechanic was planned for Generation II but scrapped to return later in Generation IV.

There were plans to have a skateboard as a type of transportation similar to the bicycle, but it was later cut for an unknown reason.

Olivine City has a hidden map/house that is only accessible by using cheat codes.
The map is of a small house containing two NPCs. The first is a Rhydon, whose glitched sprite changes into a Clefairy during walking animations. When A is pressed in front of it, it simply says, "Gugooh!" The next is a woman, when A is pressed in front of the woman in the house, she says: "When my Pokémon got sick, the Pharmacist in Ecruteak made some medicine for me." It is worth noting that she says that the pharmacy is located in Ecruteak City, when in the final version of the game it was located in Cianwood City.

Also, presuming that the player is in the Olivine House; if the radio is playing "The Pokédex Show" instead of the "Pokédex Talk Show" the game will not display any Pokédex entries and freeze (this will occur between 4am and 10am).

Pokemon Gold and Silver were planned to be the last Pokemon games.

The original starting town in Gold and Silver was called "Silent Hills". It's not known why the location changed, but it could have been to avoid comparisons to the horror game Silent Hill, which was released during Gold and Silver's development.

The gym in Goldenrod City is laid out in the shape of a Clefairy.

A Safari Zone was originally planned to be in the game, but removed at some point in development. As such, if accessed via a glitch or cheating device, there are no Pokemon to be found in the grass, but some can be found via fishing.