Note if the drive is in use, then the conversion will happen at next boot.
convert x: /fs:ntfs
Note when converting in WinNT4/2k/XP the partition will get a cluster size of 512 bytes, which will give limited performance (4 KByte is usual the optimal) More Info MS KB231756.
Note when converting in WinNT4/2k/XP the MFT will become shattered all over the partition, causing low performance.
Note the WinXP Deployment Tools can be be used to install on FAT16/FAT32 and then later convert to NTFS without getting a fragmented MFT and a 512 bytes cluster size. The utility cvtarea can reserve a continuous section of the partition which can be used by the MFT. The utility oformat can format the partition and align FAT data clusters at the cluster size boundary so the cluster size will become 4 KByte.
Note when converting a FAT16/FAT32 partition to NTFS, then permissions will not be configured. Therefore if converting the system drive, then one should make sure to configure the NTFS permissions after the conversion. More Info MS KB266118
Note if the drive contains bad sectors (Use Chkdsk to see) then the conversion will fail, and it will require a full backup of the drive and then a NTFS format to do the conversion.
Note faster boot times will be gained when only having NTFS partitions, as Win2k/WinXP reads the entire File Allocation Table (FAT) for all FAT16/FAT32-partitions found during bootup.
More Info MS KB156560
More Info MS KB214579
More Info MS KB295723
More Info MS KB307881
More Info MS KB314097