The system operated PC DOS 2.11 as well as Microsoft Disk BASIC and Microsoft Advanced BASIC. Like the PC, if the system was left to boot without inserting a diskette into one of the drives the Microsoft Cassette BASIC interpreter would be loaded, which was compatible with IBM PCjr BASIC, including Cartridge BASIC. PC DOS 2.11 could only use half of the tracks of a 3.5" drive, however, since it didn't really understand what a 3.5" drive even was. The PCjx's BIOS could only address the first 40 tracks, like a 5.25" drive.