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They both have pros and cons, but from a security perspective, you should choose NTFS. FAT32 does not offer any sort of file or folder security.

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Posted by waqasahmad

Please visit the following link:

http://cquirke.mvps.org/ntfs.htm

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Posted by sagitraz

NTFS has always been a more powerful file system than FAT and FAT32. Windows 2000, Windows XP, and the Windows Server 2003 family include a new version of NTFS, with support for a variety of features including Active Directory, which is needed for domains, user accounts, and other important security features. For more details about features in NTFS, see NTFS.

FAT and FAT32 are similar to each other, except that FAT32 is designed for larger disks than FAT. The file system that works most easily with large disks is NTFS.

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Posted by eric