Intergovernmental regional cooperation is one of the defining characteristics of political Europe. This article investigates it in the area of higher education and research. Specifically it explores what types of intergovernmental regional alliances exist and to what extent their member countries coordinate their higher education and research policies. The article focuses on six most prominent and most formalized intergovernmental regional alliances: the Benelux, Norden–The Nordic Cooperation, the Visegrád Group, the Franco-German Cooperation, the Western Balkans, and the Baltic Cooperation. There has been much research devoted to study of policy diffusion from the European to the national level, but the intergovernmental regional level has largely been ignored. This article argues that there clearly exists a multi-level governance system in the area of higher education and research, in which regional intergovernmental alliances also perform policy coordination. Therefore, the politics of European higher education policy-making cannot be fully understood by ignoring intergovernmental regional cooperation.