The mounting phenomenon of differentiated integration in the EU has hitherto been studied mainly with regard to its drivers and legal configuration. Taking the existence of differentiated integration as a given, a conceptual framework is developed for analysing its governance in practice and the conditions under which this is effective and legitimate. Referring to examples from monetary integration and Justice and Home Affairs, the framework emphasises the interplay between the legal and organisational dimensions of differentiated integration, between commitment to common policies and opportunities for participation in their development and implementation. This includes measures for assessing and conditions for explaining the effectiveness and legitimacy of differentiated integration.