The subject of this paper is the medieval and novel persecution of the witches conducted by church inquisition as well as many secular courts. Persecution of witches in Croatia has marked European, as well as Croatian history, and this period is considered justifiably to be one of the darkest periods of human history. In the Middle Ages there was a widespread fear of witches and wizards and of their misdeeds, so they began to persecute and subject to criminal proceedings. Considering how the persecution of witches was long-lasting, and how much fear and horror it has brought, it is not surprising that even today some people have stories and certain beliefs about witches that cause discomfort and fear of the unknown. The practice of the Inquisition Courts, as extraordinary papal tribunals, and mediaeval literature derived from that practice, had a great impact on the development of the criminal process and criminal procedural law and on the formation of the general European inquisition process of secular courts. The end of persecution in the middle of the 18th century contributed to the advancement of science, but also to the changing lifestyles of people. Cities have become the center of social life, and the dependence of man on theological beliefs has gradually diminished.