In this working paper we explore the independence of European Union (EU) agencies from an institutionalist perspective. Drawing on Principal Agent-theory, we first offer a definition of formal independence of EU agencies. Having specified the concept of formal independence, the second part provides an operationalisation of the concept, which captures the agencies’ mandate as well as different mechanisms of ex ante and ex post control. Thirdly, we employ our operationalization of agency independence and apply it empirically to twenty-nine EU agencies. For this purpose we present an index to assess the degree of independence of the different EU agencies. In the last section we relate our discussion on agencies’ independence to different conceptuali-sations of accountability.