More specialized Poké Balls were introduced in this game. For example, a Lure Ball is more effective if used against a Pokémon caught with a fishing rod, and a Friend Ball will make a Pokémon more comfortable and friendly to its trainer much quicker. To obtain these balls, Apricorns must be picked from special plants found throughout Johto, and Kurt in Azalea Town will fashion these into the different balls based on their color. However, Kurt can only make one ball at a time, and players must wait until the next day for Kurt to finish the ball. Although these specialized Poké Balls and Apricorns were not in future generations, there were other specialized balls.

The game introduces shiny Pokémon, i.e. Pokémon which have a different coloring than normal Pokémon of their species, and which appear very rarely (estimated to be a 1/8192 chance). In this second generation of games (though not the third generation which followed on GBA), these Pokémon often have better stats than regular non-shiny Pokémon, but can never get the maximum stats for that species. There is one exception to the shiny Pokémon system: A Red Gyarados can be found at the Lake of Rage. Since it is part of the storyline, it is impossible not to encounter this Pokémon.

The Pokérus (Pokémon virus) was introduced. The virus is even rarer (About a 1 in 32768 chance) to get than a "shiny" Pokémon, and raises the amount of stats that the playerââ‚&A » circ;¬Ã¢â€