Decisions of international institutions are not always based exclusively on intergovernmental concord. Their decision-making processes can be supranational as well, while the realization of all decisions still remains predominantly in the hands of participating states. This article is an exploration of regional governance institutions, endowed with supranational quality or traits, from viewpoint of formally sovereign states taking part in them. Political institutionalism is serving as a theoretical basis for this research. It allows focusing on institutions which structure the activity, going beyond national realm. Particular attention is paid to the practices of the EU as the most advanced supranational organization in the world. A supranational quality cab only be acquired by a multilevel political organization. Institutions of the EU are compared in this article to those of the African Union and the Eurasian Economic Union with an aim to make a judgment as concerns their adequacy to the requirements of normative and/or decisional supranationalism. The subsidiarity principle emerges as of central importance in regulating the sharing of competences between supranational institutions and national governments. Two conclusions are deemed most important in this respect. First, it seems unjustified to believe, as in the past, that supranationality always develops linearly, beginning with a decentralized system which then starts to gain in its centralization. Today we can speak of a possibility of bidirectional transformations of multilevel systems, involving supranational institutions and national governments. Second, under the influence of politicization the multilevel governance in the EU in particular is changing its outlines – it becomes postfunctionalist and is being democratized. For such a system, with its newly emerging outlook, rigorous control of the observance of subsidiarity is relatively losing in importance, while supporting its throughput legitimacy (procedural transparency and accountability) becomes a more prominent task.