FAT (FAT16 and FAT32) and NTFS are two methods for storing
data on a hard drive. The hard drive has to either be
formatted using one or the other or can be converted from
one to the other (usually FAT to NTFS) using a system tool

NTFS is a high-performance and self-healing file system
proprietary to Windows XP 2000 NT which supports file-level
security compression and auditing. It also supports large
volumes and powerful storage solution such as RAID.
The most important new feature of NTFS is the ability to
encrypt files and folders to protect your sensitive data

NTFS stands for New Technology File System
And 
Fat  stands for File Alocation Table

NTFS IS HTE FILES SYSTEM IT SUPPORTS IN ONLY NT technology
But FAT is supported by all the file system even with linux

FAT(FAT16/FAT32) FAT16 have create the partition only 2GB in win 98 and 4GB in winxp.
FAT32 have create the partion upto 32GB
FAT stands for (file allocation table) it is way to storing the data in hard drive.

NTFS(new technology file system)is high features compare to FAT it is features file,folder securty encryption data and create the partition unlimited space.