The fundamental aim of Justinian's church policy from the very beginning of his reign was the establishment of closer relations with Rome; hence he had to appear as the defender of the Council of Chalcedon, the decisions of which were strongly opposed by the eastern provinces. During Justinian's reign the see of Rome enjoyed supreme church authority. In his letters to the bishop of Rome, Justinian addressed him as Pope, Pope of Rome, Apostolic Father, Pope and Patriarch, etc., and the title of pope was applied exclusively to the bishop of Rome. In one epistle the Emperor addressed the Pope as the head of all holy churches (caput omnium sanctarum ecclesiarum), and in one of his Novels he definitely stated that the most blessed see of the archbishop of Constantinople, the New Rome, ranks second after the most holy apostolic see of Old Rome.
Justinian came into collision with the Jews, the pagans, and the heretics. The latter included the Manichaeans, the Nestorians, the Monophysites, the Arians, and representatives of other less significant religious doctrines. Arianism was widely spread in the West among the Germanic tribes. Survivals of paganism existed in various parts of the Empire, and the pagans still looked upon the Athenian school as their main center. The Jews and the followers of minor heretical movements were centered primarily in the eastern provinces. The widest following was, of course, the Monophysitic. The struggle with the Arians in the West assumed the form of military undertakings, which ended in the complete or partial subjection of the Germanic kingdoms. In view of Justinian's conviction of the necessity of a unified faith in the Empire there could be no tolerance toward the leaders of other faiths and heretical teachings, who consequently were subjected during his reign to severe persecution carried out with the aid of military and civil authorities.