Check the event viewer on the Domain controllers during the issue (or if you have an idea of the time frame, then you should be able to find any related issues). I'd check the application, system, and security event viewers. See if you have any failed logins during the time period, as this will tell you if the domain controller is actually responding to requests or not. If the issue seems to happen around the same time, or at least once a day, try setting up perfmon on the server to make sure that it's not an issue with a scheduled task or resource contention or anything like that.
You may also need to check the network. if possible, put a laptop in your rack temporarily, or login from a server that is on the same switch as the domain controller. This will help you determine if it is a network issues (possibly a bad switch/router, or a bad cable somewhere in the mix. You may need to work backwards while the issue is happening.
Without more information on the issue, it's hard to pinpoint a good troubleshooting step so you'll have to start pretty broad since there could be any number of reasons why your seeing this issue.