Equality institutions are major arenas for analyzing political intersectionality. This article looks at equality institutions in the context of European equality policy changes since 2000 and argues for an institutional typology that differentiates gender equality machineries from anti-discrimination bodies and consultative equality bodies. These functionally different equality institutions build up into larger equality institutional architectures in which the different components serve complementary strategies in pursuing complex gender equality policies. Equality institutional architectures vary in how they institutionalize the relationships between gender inequality and other inequality categories. Layered, hierarchical, and integrated models of equality institutional architectures are identified as different in institutionalizing the intersections and hierarchies of different inequality axes. The article argues that analyzing equality institutions through such a conceptual framework contributes to a more nuanced research agenda for analyzing intersectionality in policy practice, one that could be applicable, beyond equality institutions, also to the analysis of policy texts and civil society mobilization patterns. The article illustrates the developed conceptual framework through a comparative analysis of gender equality institutional architectures emerging in the last twenty years in the ten new European Union member states of Central and Eastern Europe.