Which mainline Pokémon games were the first to feature entirely 3D graphics?

Pokémon X and Y were the first mainline Pokémon games to feature entirely 3D graphics.

Released for the Nintendo 3DS in 2013, Pokémon X and Y introduced the Kalos region, which is inspired by France. The games used fully polygonal environments and character models rather than the primarily sprite-based presentation of earlier mainline entries.

They also introduced Fairy-type Pokémon, Mega Evolution, character customization, and new ways to interact with Pokémon. Their 3D presentation represented a major visual change while retaining the series' turn-based battles, exploration, collecting, and version-exclusive Pokémon.

Earlier titles had already used 3D elements in menus, battle effects, or spin-off games such as Pokémon Stadium. That is why “first 3D Pokémon game” can be misleading. X and Y specifically hold the distinction for being the first mainline games with entirely 3D graphics.