- It can defragment only local volumes.
- It can defragment only one volume at a time.
- It cannot defragment one volume while scanning another.
- It cannot be scheduled.
- It can run only one Microsoft Management Console (MMC) snap-in at a time.
- It cannot defragment NTFS volumes with cluster sizes larger then 4 kilobytes (KB) in Windows 2000.This limitation has been removed for Disk Defragmenter in Microsoft Windows XP and Microsoft Windows Server 2003.
- Fine-grained movement of uncompressed NTFS file data is not possible in Windows 2000. Moving a single file cluster also moves the 4-KB part of the file that contains the cluster. This limitation has been removed for Disk Defragmenter in Windows XP and later.
- In Windows 2000, it does not defragment NTFS metadata files, such as the Master File Table (MFT), or the metadata that describes a directory's contents. This limitation has been removed in Windows XP and later. It cannot defragment encrypted files in Windows 2000. This limitation has been removed in Windows XP and later.