This paper analyses the dialogue of Churches and EU institutions, with a focus on the Churches’ representations at the European Union. These representations are described in accordance with the confessional divisions: Catholic, Orthodox and Protestant. Commission of the Bishops’ Conferences of the European Union (COMECE) is regarded as the most influential Catholic representation; among the Orthodox representations this status is kept by the representation of the Church of Greece, and among Protestant—the Protestant Church in Germany (EKD). Overall, this paper finds that the existing patterns of cooperation constrain the Churches’ ability to influence the process of decision-making in the EU. However, this influence may increase should the practical cooperation on the policy level acquire more intensive forms.