The principle of autonomy of the European Union law which sparked intensive debates after Kadi-1 judgment of the European Court of Justice and its Opinion No 2/13, is widely recognized as one of the key general principles of the Union law. The article suggests that the principle of autonomy plays a crucial role in the ongoing transformation of the European Union into a sort of quasi-federation in dynamics where the Court of Justice aims to arrange a sectoral transfer of sovereign powers from the EU member-states states on the level of that quasi-federation. The results of the practical application by the Court of Justice of the EU of “external dimension” of the principal of autonomy (articulating that EU law is not a part of international law) reveals intentions of the Court of Justice independently and according to its own rules decide the issues of validity and applicability of the norms of international law in the legal order of the European Union. The same must be said about the control from the side of the EU Court of Justice of international treaties concluded by the EU member-states as subjects of such quasi-federation and by the Union itself. A remarkable similarity between arguments used by the Court of Justice of the EU in such issues and reasoning of national constitutional courts of some European countries provides feasible grounds for an assumption to consider the EU Court of Justice as a sort of constitutional court of emerging quasi-federation which protect and secure a gradual sectoral transfer of sovereignty from the EU member states on the Union level. But it should not be taken as a legal autarchy from the side of the EU or a construction of insurmountable wall between EU law and international law. It is better to be views as a right of the Court of Justice of the EU to determine how international legal obligation of the EU or its member- states may affect autonomy of the EU legal order. From this point of view any accusations addressed to the Court of Justice of the EU in adding further fragmentation of international law look as missing a point because the Court of Justice takes European Union law as law of emerging quasi-federation, not as international law.