In charge of European police and judicial co-operation respectively, Europol and Eurojust are tasked with facilitating exchange of information, providing support to member states in co-ordinating operational activities. While ‘cooperation’ or ‘coordination’ agencies endowed with ‘some’ operational powers but lacking decision-making powers, they are, at least by virtue of their formal tasks and competences, two of the most powerful EU bodies operating in the area of freedom, security and justice. The present paper investigates the evolution of these agencies, focusing on their actual autonomy, the extent to which they have been able to harness and expand upon the powers granted by formal design, as well as the accountability arrangements in place to hold them in check and ongoing practices in this regard. From both an autonomy and accountability perspective, a study of the development of these bodies is highly relevant, particularly given the political nature and high sensitivity of the fields in which they operate, and the close association of their objectives and tasks with key aspects of national sovereignty.