In Opinion 2/13 the Court of Justice of the European Union found that the draft agreement on the EU’s accession to the European Convention on Human Rights was “liable adversely to affect the specific characteristics of EU law and its autonomy.” The Court in recent years has applied the principle of autonomy – a concept first developed regarding the relationship between the EU and its Member States – to the EU’s relationship with third states and international organizations. The EU’s increased interaction with external actors raises questions regarding the effects this might have on the integrity and unity of EU law and the EU legal order. What exactly does the principle of autonomy entail in EU external relations law? This Working Paper examines the case-law in which the Court has applied the principle of autonomy and argues that the principle is a more broad and all-compassing structural principle than is often presented. The Court’s focus is almost entirely on what might be called the negative dimension of autonomy; it is about ensuring that the EU legal order is protected from external threats. It is less concerned, however, with the positive dimension of autonomy, which entails providing the EU with the ability to act effectively as a distinct actor on the international stage.