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With regard to the relations with the Serb Orthodox Church, Pope John Paul II could not escape the controversy of the involvement of Croatian Catholic clergy with the Ustasa regime of World War II. He beatified Aloysius Stepinac in 1998, the Croatian war-time archbishop of Zagreb, a move seen negatively by those who believe that he was an active collaborator with the Ustaše fascist regime. On June 22, 2003, he visited Banja Luka in Bosnia and Herzegovina, a city inhabited by many Catholics before the 1992-1995 war, but since then predominantly Orthodox. He held a mass at the Petrićevac monastery, a place of considerable controversy and distress, both during the World War II and during the Yugoslav wars.
The Pope had been also saying during the entire pontificate that one of his greatest dreams was to visit Russia, which never actually happened. He had made several attempts to solve the problems which arose during centuries between the Roman Catholic Church and Russian Orthodox Church, like giving back the Kazan Icon of the Mother of God in August 2004. However, the Orthodox side was not that enthusiastic, giving statements like: "The question of the visit of the Pope in Russia is not connected by the journalists with the problems between the Churches, which are now unreal to solve, but with giving back one of many sacred things, which were illegally stolen from Russia." (Vsevolod Chaplin). There were also statements saying that the icon which was returned was one of four copies made of the original icon, which is still in an unknown location.