The Independent State of Croatia (Nezavisna Država Hrvatska –NDH) was a Nazi puppet state that existed from April 1941 until May 1945. It was governed by the Ustasha movement, an extreme right-wing and racist political organization of Croatian nationalists. According to the Ustasha ideology, NDH had to become a strictly Croatian and predominantly Catholic state. To fulfill this political vision, in a country where Croats barely made a population majority, Ante Pavelić and his associates turned to genocide, systematically organizing mass pogroms of Serbs, Jews, and Roma. The Catholic Church, as the leading and historically most influential religious organization among the Croats, wasn’t a mere bystander in these events. It enjoyed a mutually beneficial and cordial relationship with the Ustasha regime and actively participated in the process of state-building, including various crimes against Serbian civilians. This paper, based on primary historical sources from Croatian, Serbian, and the Vatican’s archives, explores the Catholic Church’s involvement in the NDH genocide.