This final paper deals with inquisition as a churches weapon in the war against heretics. In the 12th century wave of the heretical movements took over the Europe ,caused by the hedonistic life of the priests who did not fulfill their duties. Main threat to Roman Church were Cathars, Patarenes, Bogomils, Bosnian Christians, Brothers of free spirit and Waldensians. Pope Innocent III. even invoked the war against Cathars , later called Albigensian Crusade. The war that begun for religious reasons will eventually turn into a war for independence of South France. Due to unstoppable breeding of heresy pope Lucius III., in agreement with Friedrich I. Barbarossa, established episcopal courts to suppress heresy. But these courts were not efficient so in 1232.pope Gregory IX brought decree Ille humani generis which led to Papal inquisition conducted by Dominicans. One of the main roles of inquisition was to establish proper procedures and methods. The most famous inquisition was Spanish inquisition which was used by a royal couple Ferdinand and Isabelle in their fights with Moors and Jews. The most famous Spanish inquisitor was Tomas de Torquemada. With the time witchcraft became one of the main issues for inquisition. Main target became women, inquisitors Heinrich Kramer and Jacob Sprenger wrote a book Malleus Maleficarum which contained the entire system of witchcraft and witches. In Croatia Dominicans run inquisition against Bosnian Christians.