File Allocation Table (FAT): FAT is a simple file system with limited reliability and performance capabilities. NT's FAT file system is a long filename (LFN)-capable version of the one in DOS. FAT volumes in NT can be up to 4GB; DOS can address only up to 2GB. FAT is required for volumes that must access DOS and NT in dual-boot configurations.

NT File System (NTFS): NTFS is a highly reliable, secure, and tuned file system capable of supporting volumes up to 16 exabytes (EB). Filenames on NTFS volumes are Unicode-compliant long filenames stored with 8.3 FAT-type filenames for backward compatibility with DOS machines accessing networked NTFS volumes. NTFS also supports fault-tolerance features such as transaction-based recovery and hot-fixing bad disk sectors. NTFS is far less prone to file fragmentation than FAT. NTFS's superior reliability and security features make it ideal for server drives or large volumes (more than 400MB).

High-Performance File System (HPFS): HPFS first appeared with OS/2 1.2. HPFS provides superior capabilities to FAT, including support for long filenames and volumes of up to 2048GB. HPFS uses physical sectors rather than clusters as allocation units. Physical sectors increase storage efficiency and reduce file fragmentation compared to FAT. The OS/2 version of HPFS supports hot-fixing bad sectors, but the NT version does not. Unlike NTFS, HPFS doesn't support security or transaction-based disk recovery. NT 4.0 does not support HPFS.

CD-ROM File System (CDFS): CDFS is a read-only file system for CD-ROMs. Macintosh and PC-compatible systems use two different CDFS formats that are incompatible (however, NT Server lets you share a PC CDFS volume with Mac clients).