Offline defragmentation of NTDS.DIT should remove unused portions of the database and reduce its' overall size.

In addition to being larger, both the used and unused space continues to grow on your Windows 2000 server.

NOTE: See The size of the Active Directory database differs on various domain controllers?

If you have not applied Service Pack 3, or Service Pack 4, inefficiencies in the Microsoft Jet database engine may cause this behavior in some scenarios.