Religion has often been condemned for having been a source of war and conflict rather than a vehicle of peace. For more than 1500 years religions, through their various institutions, have been influenced the state and its politics. Today, most of the modern countries claim that religion has no more space in the public arena. Also they consider it very difficult to go back to an era when the religious institutions treated the state as its instrument. But, in spite of those claims, Samuel Huntington sees religion as a main cause of contemporary wars. This work explores the role played by religions in Balkan and Caucasus conflicts and seeks to assess the validity of the Huntington's "Clash of Civilizations" theory in these wars.