OS/2 has three supported file systems: FAT, HPFS, and HPFS386.
The OS/2 2.0+ implementation of FAT is 32-bit and gets slightly higher performance than the HPFS file system shipped with OS/2 2.0+. However, when a large number of files is created and destroyed on a FAT file system, it tends to get fragmented more than a similiar HPFS file system would.
The normal HPFS that is shipped with OS/2 2.0 and above is still 16-bit. There are some rumors that IBM will ship HPFS386 with OS/2 eventually, however. HPFS smart caching takes up more memory than a FAT system.
HPFS386 comes with IBMs Lan Server Advanced. It is fully 32-bit and gives a 10-15% performance gain over the regular version of HPFS. Lan Server does not have to be used on the OS/2 system, but it must be installed and a license purchased to legally use HPFS386.