With the rising fear of Islamisation in Europe and increasing Islamist sentiment in Turkey, the issue of religion in the context of integration of Turkey into the European Union remains relevant. After a long-lasted wait and continuous negotiations, Turkey seems to be moving further away from getting accepted in the EU. The research focuses on the religious factor in this unrelenting friction between the two regions / entities and answers the question as to why the EU and Turkey should consider religion as one of the variables in the European integration. The analysis is done with the use of primary and secondary sources with special focus on Samuel Huntington’s realism-inspired work ‘Clash of the Civilization.’ Turkish sources were used for better understanding the dynamics of Turkey. In terms of methodological approach the research is done with using the content analysis and contemporary observation of socio-political scenario and behavioral changes that the EU and Turkey going through. The authors conclude that there is no proper mechanism to consider religion as a variable, but psychologically it is still playing a major role in both the EU and Turkey. The authors believe that the EU and Turkey should discuss the religious dimension of integration while talking other dynamics.