Earlier in the 4th century, following the Diocletianic Persecution of 303–313 and the Donatist controversy that arose in consequence, Constantine had convened councils of Christian bishops to define the orthodoxy, or "correct teaching", of the Christian faith, expanding on earlier Christian councils. A series of ecumenical councils met during the 4th and 5th centuries, but Christianity continued to suffer rifts and schisms surrounding the issues of Arianism, Nestorianism, and Miaphysitism. In the 5th century the Western Empire decayed as a polity: invaders sacked Rome in 410 and in 455, and Odoacer, an Arian barbarian warlord, forced Romulus Augustus, the last nominal Western Emperor, to abdicate in 476. However, apart from the aforementioned schisms, the church as an institution persisted in communion, if not without tension, between the east and west. In the 6th century the Byzantine armies of the Eastern Roman Emperor Justinian I recovered Italy and other sections of the western Mediterranean shore. The Eastern Roman Empire soon lost most of these gains, but it held Rome, as part of the Exarchate of Ravenna, until 751, a period known in church history as the Byzantine Papacy. The Muslim conquests of the 7th century would begin a process of converting most of the then-Christian world in West Asia and North Africa to Islam, severely restricting the reach both of the Byzantine Empire and of its church. Missionary activity directed from Constantinople, the Byzantine capital, did not lead to a lasting expansion of the formal power of the Empire's state church, since areas outside the empire's political and military control set up their own distinct state churches, as in the case of Bulgaria in 919.
Justinian I, who became emperor in Constantinople in 527, established the bishops of Rome, Constantinople, Alexandria, Antioch, and Jerusalem – referred to as the Pentarchy – as the leadership of the Imperial church and gave each bishop the title of "Patriarch". However, Justinian saw these bishops as under his tutelage: according to his arrangement, "the Emperor was the head of the Church in the sense that he had the right and duty of regulating by his laws the minutest details of worship and discipline, and also of dictating the theological opinions to be held in the Church". However, by Justinian's day, the churches that now form Oriental Orthodoxy had already seceded from the Imperial state church, while in the west Christianity was mostly subject to the laws and customs of nations that owed no allegiance to the Emperor in Constantinople. While eastern-born popes who were appointed or at least confirmed by the Eastern Emperor continued to be loyal to him as their political lord, they refused to accept his authority in religious matters, or the authority of such a council as the imperially convoked Council of Hieria of 754. Pope Gregory III (731-741) became the last Bishop of Rome to ask the Byzantine ruler to ratify his election. By then, the Roman Empire's state church as originally conceived had ceased to exist. In the East, only the largest fragment of the Christian church was under the Emperor's control, and with the crowning of Charlemagne on 25 December 800 AD as Imperator Romanorum by the latter's ally, Pope Leo III, the de facto political split between east and west became irrevocable. Spiritually, the Chalcedonian Church, as a communion broader than the imperial state church, persisted as a unified entity, at least in theory, until the Great Schism and its formal division with the mutual excommunication in 1054 of Rome and Constantinople. Where the Emperor's power remained, the state church developed in a caesaropapist form, although as the Byzantine Empire lost most of its territory to Islam, increasingly the members of the church lived outside the Byzantine state. The Eastern Roman Empire finally collapsed with the Fall of Constantinople to the Islamic Ottoman Turks in 1453.
Western missionary activities created a communion of churches that extended beyond the empire, the beginnings of which predated the establishment of the state church. The obliteration of the Empire's boundaries by Germanic peoples and an outburst of missionary activity among these peoples, who had no direct links with the Eastern Roman Empire, and among Pictic and Celtic peoples who had never been part of the Roman Empire, fostered the idea of a universal church free from association with a particular state. On the contrary, "in the East Roman or Byzantine view, when the Roman Empire became Christian, the perfect world order willed by God had been achieved: one universal empire was sovereign, and coterminous with it was the one universal church"; and the state church came, by the time of the demise of the Byzantine Empire in 1453, to merge psychologically with it to the extent that its bishops had difficulty in thinking of Christianity without an emperor.
Modern authors refer to this state church in a variety of ways: as the catholic church, the orthodox church, the imperial church, the imperial Roman church, or the Byzantine church, although some of these terms are also used for wider communions extending outside the Roman Empire. The legacy of the idea of a universal church polity carries on, directly or indirectly, in today's Catholic Church and Eastern Orthodox Church, as well as in others, such as the Anglican Communion.
Before the end of the 1st century, the Roman authorities recognized Christianity as a separate religion from Judaism. The distinction, perhaps already made in practice at the time of the Great Fire of Rome in the year 64, was given official status by the emperor Nerva around the year 98 by granting Christians exemption from paying the Fiscus Iudaicus, the annual tax upon the Jews. Pliny the Younger, when propraetor in Bithynia in 103, assumes in his letters to Trajan that because Christians do not pay the tax, they are not Jews.