FAT16

In November 1987, Compaq DOS 3.31 (an OEM version of MS-DOS 3.3 released by Compaq with their machines) introduced what is today called the FAT16 format, with the expansion of the 16-bit disk sector count to 32 bits. The result was initially called the DOS 3.31 Large File System. Although the on-disk changes were minor, the entire DOS disk driver had to be converted to use 32-bit sector numbers, a task complicated by the fact that it was written in 16-bit assembly language.

In 1988 the improvement became more generally available through MS-DOS 4.0 and OS/2 1.1. The limit on partition size was dictated by the 8-bit signed count of sectors-per-cluster, which had a maximum power-of-two value of 64. With the standard hard disk sector size of 512 bytes, this gives a maximum of 32 KB clusters, thereby fixing the "definitive" limit for the FAT16 partition size at 2 gigabytes. On magneto-optical media, which can have 1 or 2 KB sectors, the limit is proportionally greater.

Much later, Windows NT increased the maximum cluster size to 64 KB by considering the sectors-per-cluster count as unsigned. However, the resulting format was not compatible with any other FAT implementation of the time, and it generated greater internal fragmentation. Windows 98 also supported reading and writing this variant, but its disk utilities did not work with it.

The number of root directory entries available is determined when the volume is formatted, and is stored in a 16-bit signed field, defining an absolute limit of 32767 entries (32736, a multiple of 32, in practice). For historical reasons, FAT12 and FAT16 media generally use 512 root directory entries on non-floppy media. Other sizes may be incompatible with some software or devices (entries being file and/or folder names in the original 8.3 format).[12] Some third party tools like mkdosfs allow the user to set this parameter.