The creation and empowerment of European Union (EU) agencies constitutes one of the most momentous developments of the EU composite administration. In the last decades, the delegation of powers to EU agencies grew exponentially both in quantitative and qualitative terms. As a result of this evolution and of the more permissive position of the Court of Justice of the EU in the Short selling judgment, EU agencies today are called upon to make relevant political, economic and social choices even in highly sensitive and contentious domains. The possibility to challenge their acts has been finally sanctioned in primary law. The exercise of their powers, however, is subject only to a limited scrutiny by the Court, which has recognized broad discretion to these bodies in carrying out complex and technical assessments. Analysing the approach of the Court to the review of European Chemical Agency’s (ECHA) discretion, this paper reflects upon its effectiveness and its implications for the accountability and legitimacy of agencies within the EU institutional framework.