The Nintendo DS has two slots for game cartridges: Slot 1, on the top of the system is used for Nintendo DS games, whilst Slot 2 on the bottom of the unit is used for the larger Game Boy Advance cartridges. However, due to a slightly amended form factor and the absence of the Zilog Z80-like processor, the DS may not be used to play games for the original Game Boy or the Game Boy Color. In addition, the DS does not have a port for the Game Boy Advance Link Cable, which means that multiplayer or GameCube-Game Boy Advance link-up modes are not available in Game Boy Advance titles.

In some cases, Nintendo DS games inserted into Slot 1 can detect the presence of specific Game Boy Advance games in Slot 2, which may allow extra content can be unlocked or added. This may be achieved by starting the Nintendo DS game with the appropriate Game Boy Advance game inserted. There is also Wi-Fi mode on some GBA games.

When playing Game Boy Advance games, the Nintendo DS only uses one screen, which the player can configure to either the top or bottom screen. Due to the slightly different screen resolution between the two systems - 240 × 160px (0.04 megapixels) for the Game Boy Advance and 256 × 192px (approx. 0.05 megapixels) for the Nintendo DS, GBA games are displayed within a black border on the screen.