The European Union has a comprehensive legal framework in place for the authorization, traceability, and labelling of genetically modified organisms, the aim of which is to create a unified market while simultaneously ensuring that the placing on the market of the products concerned will not pose a risk to human or animal health or to the environment. This framework sets out complex, multi-level procedures which entail the cooperation and sharing of information between various national and European authorities. Filling a gap in the literature, this contribution focuses on the challenges to the system of judicial accountability that emerge in this particular system of multi-level administration. This Article shows that the problems posed by composite procedures in terms of access to justice and effective judicial protection can possibly be solved in light of the current rules concerning the division of labor between national and European courts and the applicable case law of the Court of Justice. As this Article will show, many more unsolved issues arise instead with respect to the compliance with the requirements of access to justice provided by the Aarhus Convention.