The need for EU agencies’ expertise in policy-making is increasing in the areas characterized by complexity, uncertainty and risks. While most studies in EU agencies focus on the legitimacy, accountability and autonomy, we know little about their de facto influence on European policy-making based on expertise they provide as policy input. Officially, EU agencies function as advisory bodies, and policy-makers are not legally obliged to follow agencies’ opinions. But, does this role separation happen in reality? How and to what extent do EU agencies make their voices heard by policy-makers in the European policy-making process? By focusing on the production and dissemination of expertise, this article examines the conditions under which EU agencies function beyond mere non-binding advisory role. The empirical results are drawn based on the analysis of two cases of the European Medicines Agency and the European Centre for Disease Prevention and Control in the health policy domain.