This paper takes the view that Christian Churches should be regarded as special participants of European integration. Churches embrace features of non-state actors and identity formers, and they take a unique stance as contributors to the initial stages of the integration process. In addition, Churches perform their functions within the Church-State regimes—the phenomena, unknown to other actors of European integration. Overall, Christian Churches have established themselves as unique and influential participants of European integration/EU politics. The concrete aspects of the Churches’ participation are analysed via their contribution to the process of the latest reform of the EU treaties (2001-2009). The focus is on three main stages of the reform’s process: the Constitutional Convention, the Inter-Governmental Conference and the Treaty of Lisbon. The presence of Churches was visible at every stage, but with a different degree of involvement. Churches managed to gain support of some influential politicians and some leaders of Member States/Candidate Countries, although the outcome was not as favourable for them as one could expect. Nevertheless, this outcome confirmed the unique and influential role of Churches in European integration/EU politics.