The term FAT is used to describe the file system used by Microsoft® MS-DOS, Windows® 9x and Windows® ME operating systems. Specifically, the file allocation table is the index used by the operating system to keep track of the clusters (a group of disk sectors) belonging to each file stored on a disk. Clusters are the basic unit of logical storage used by the operating system: and the FAT is required because the clusters belonging to a file may not be stored contiguously. When a file is written to the disk, the operating system creates a FAT entry for the file: this notes the location of the file’s start cluster and its overall size. When access to the file is later required, the operating system can then piece together each cluster belonging to the file and load the file into memory for processing.

Alternative file systems are NTFS, used by Windows® NT, Windows® 2000 and Windows® XP, and HPPS [High Performance File System] used by OS/2.