Book excerpt: In this paper, we address the perennial challenge that underlies the governance of European Union agencies - as well as rendering it an inherently political issue: the balance between the autonomy of agencies, arguably the crucial ingredient for the effective operation of this model, and the accountability they must render, critical to their legitimacy (and that of the EU more generally). We trace how, across the board, the autonomy and accountability of EU agencies has developed, to what extent early expectations have been matched or challenges have arisen.