In Uganda, contested relations between the central government and sub-national regions have, since independence, shaped state formation and national identity in fundamental ways. Today, the country is characterised by regionally uneven state presence, and distinct sub-national identities and ongoing contestation over territorial demarcations, loci of authority and political identities. This article explores the politics of territory, identity and authority in three Ugandan regions in this context, in order to analyse the implications for exclusion and conflict at the sub-national level. This involves struggles over the territorial and administrative demarcations of and within regions; the loci and scope of authority with regards to these units; struggles over access to land; and the (non-)recognition of various cultural–political identities in these regions.