The delegation of policy-making tasks to EU agencies and their remarkable growth in number over the past two decades mark a striking new development in the EU's institutional make-up. While most of the nascent literature on the EU's ‘agencification’ addresses the conditions for agency creation and the implications of agency governance from the perspective of democratic accountability, there is a lack of empirical research systematically scrutinising the institutional structure and degree of formal-institutional independence of these agencies. This article offers a comprehensive empirical assessment and measure of the variation in institutional independence displayed by the entire set of 29 EU agencies operating under the EU's three pillars and tests hypotheses explaining variation in formal independence among agencies.