Active directory performs it’s own maintenance every 12 hours automatically. However, this alone is not enough to keep a clean and healthy database. The database must also be compressed and defragmented. To do this perform the following steps.
1. Reboot your server and push F8 to go into Directory Services Restore Mode.
2. Login as usual.
3. Create a temporary directory. c:NTDS
4. Open a command prompt and type ntdsutil files
5. You should get a prompt file maintenance: From here type in compact to c:NTDS
6. If the compact was successful copy the ntds.dit file to the %systemroot%NTDS directory.