Here is a good post by Nino Bilic on the compatibility of E2K3 (32bit) running on Windows Server 2003 x64.
It seems like a question of compatibility / incompatibility of current versions of Exchange (mainly Exchange 2003) and Windows Server 2003 x64 editions is coming up more and more, so let’s address it.
In short – running current versions of Exchange, including Exchange 2003 on Windows Server 2003 x64 editions is not supported.
In fact, Exchange 2003 does not even install properly under WOW64. There are several reasons for this – some are related to Exchange 2003 IIS dependency but the biggest problem is that Exchange Setup installs the IFS (Installable File System) driver (exifs.sys) which is a 32 bit driver. On x64 editions of Windows, all of the Kernel mode components (which includes drivers) have to be native 64 bit components, while the User mode applications can be run under WOW64. This problem can not be addressed in future Exchange 2003 Service Packs either.
Now – the future is bright, we have plans, just not with current versions of Exchange. There is a list of applications that will run under Windows Server 2003 x64 in either 32 bit compatible or 64 bit native mode and you can find it here.
For more information on Exchange 2003 installation requirements, please go to this page.