Despite over seventy years of common history of Czechoslovakia, including the same religious policy and the same religious legislature, after disintegration this state in 1993, relations between states and churches formed differently in Czech Republic and Slovakia. The Czech Republic is one of the most secularized European states with the highest rate of atheists in the confessional structure. Only third part of Czechs believe and the largest churches are the Roman Catholic Church, the Evangelical Church of Czech Brethren and the Czechoslovak Hussite Church. In Slovakia the level of religiousness among the citizens is still quite high. Above facts determinate contemporary religious policy and place church and religion in both new states. The aim of the present article is to look at religious relations in the Czech Republic and Slovakia in comparative perspective.