Despite being invoked by the Court in landmark cases from Van Gend en Loos and Kadi to Pringle and Opinion 2/13, autonomy has remained an elusive concept in EU law. This article suggests that it is applied by the Court to make three distinct yet related claims; first about substantive and institutional independence of the EU and EU law; secondly about the systemic integrity of the EU legal order; and thirdly about the standards that need to be upheld in the EU as a constitutional legal order. As such, autonomy is shown to have different meanings and connotations besides policing the openness of EU law to other legal regimes. The ECJ�s reasoning in developing autonomy is discussed against the background of its selfreferential reliance on the principles of loyalty and effectiveness, and of the theory on the nature of general principles in EU law more broadly.