I've seen this question on the MOM newsgroups a couple of times, and it isn't immediately obvious to a newcomer: How do I get the Exchange 2000/2003 Topology diagram populated?

The answer is, add an Exchange server in your organization to the “Exchange Topology Discovery Computers” computer group in the administrator console. MOM downloads a special set of rules to the server(s) in this group which do the actual topology “discovery”.

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