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During World War II a number of Croatian Catholic priests, and some of the then bishops in the territory, cooperated with the Ustaša regime, who ran a Nazi puppet state that pursued a genocidal policy against the Serbs (who were Eastern Orthodox Christians), Jews and Roma.
Many priests not only cooperated with the regime but personally committed murders or forced religious conversions of Serbs and Jews. There have been cases where the whole population of villages was killed because they were Serb Orthodox; conversely, there have been cases where villagers were superficially converted and remained alive.
The involvement of the church as a whole is also controversial due to several meetings and public sightings of Ante Pavelić, the leader of the Ustaše, with the bishops and even the archbishop Alojzije Stepinac. On November 17, 1941, a bishops' conference was convened in Zagreb regarding the issue of mass religious conversions. The Bishopric News no. 2, 1942 subsequently recorded a directive that said "Our work is legal because it is in accord with official Vatican policy [...] that the Eastern Orthodox Church be converted to the Catholic faith".
By the end of the war, a large number of people who were in connection with the fascist regime, including many priests, fled Croatia (and many fled Europe altogether). According to some sources there were about 1,500 priests among the exiles, many of whom fled in order to escape justice.
After the war, Cardinal Stepinac was indicted by the Communist authorities for collaboration with the fascist regime. He was proclaimed guilty and sentenced to 16 years in prison. However, because his trial was politically motivated and set up, he only served five years in prison before the sentence was commuted to home arrest. He was transferred back home to the village of Krašić in Zagorje, and died shortly thereafter.