Prominently figuring in the Area of Freedom, Security and Justice, the European Police Office (Europol) and the European Union's Judicial Cooperation Unit (Eurojust) are tasked with facilitating the exchange of information and providing support to the EU member states in coordinating operational activities. This article 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. It shows that, for a long time, Europol and Eurojust have developed in different ways, both with regard to autonomy and accountability, and that the relationship between these phenomena has been anything but straightforward. Moreover, it demonstrates that design has been a necessary but not a sufficient condition for both agencies' evolution, thus putting recent formal-legal changes to the agencies' design (most notably Europol becoming a full-fledged agency) into perspective. © 2013 Taylor & Francis.