The European integration posed and is posing challenges to the more than 100 Christian churches active in the EU if they want to continue to look after their mission to go public by raising the voice of those who do not have a lobby of their own as well as to defend the status they have under national law. The paper analyzes if and how Christian churches respond with strategies of interest intermediation to ‘Brussels’ or to the "sui generis" character of the EU as a multi-level system. It is assumed that the strategies of interest intermediation differ according to the organisational patterns of the denomination family (Roman Catholic, Old-Catholic, Protestant, Anglican and Orthodox), the church-state-relation in the home country and to the policy field. Two case studies on the interest intermediation for the “article for churches” in the EU primary law and against the funding of stem cell research by the EU will complement the general findings. The paper will present empirical proof for the assumptions drawing on interviews with representatives of churches and the EU institutions as well as on unpublished documents of the Commission.