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Looking at upgrading our existing Windows 2000 Active directory domain to Windows 2003 Active directory. Have done it once on a Windows 2000 domain with no exchange server present and all went fine. Any issues that may come up when upgrading a windows 2000 domain with Exchange 2003 in it?

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Expect issues, there always are issues when doing an upgrade like this. But, in theory at least, there shouldn't be any. I would advise making sure you have a good backup of your AD before starting. – Coding Gorilla Sep 22 '11 at 19:49
@CodingGorilla This isn't really a major upgrade. Install bunch of new 2003 DCs. Wait. Transfer FSMO roles. Wait. Update DNS settings in DHCP and on anything static. Wait. Demote W2K DCs. Done. – MDMarra Sep 22 '11 at 19:53
@MarkM Yea I said the same thing to a customer a couple of weeks ago when upgrading (not in-place, completely new server) Exchange 2007 to Exchange 2010. It tooks us 9 hours that night, and they've been "cleaning it up" for the past two weeks. I always just like to plan for the unexpected. – Coding Gorilla Sep 22 '11 at 19:55
To be fair, a 2007/2010 Exchange migration is something completely different from an AD upgrade... – Massimo Sep 22 '11 at 19:57
Why ever are you upgrading to such old releases?! Server2008 is mature, and EX2010 should be stable by now... EX2003 is out of support, and Server2003 is only in Extended support. – gWaldo Sep 22 '11 at 20:26

If the upgrade is done properly, there will be no issue at all as long as Exchange is concerned.

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Is there a different forest prep that needs to be run? I thought I saw something about using the Exchange Server install cd to do the forest and domain prep, I could be mixed up though. – Matt Fitz Sep 22 '11 at 20:20
That has already been done when Exchange was installed. You'll only need to run the prep steps for Windows Server 2003. – Massimo Sep 22 '11 at 20:38
Thanks for the help Massimo, so Exchange 2003 being present in the domain should not matter. Just a little leary about screwing up the Exchange server. – Matt Fitz Sep 22 '11 at 21:35

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