The Indian Church came in contact with the East Syrian Church possibly from the 4th century. In the 5th century, the church of Persia came to its own. The Catholicos with his seat at Seleucia Ctesiphon began to be called also Patriarch and in 486 A. D. the Church officially accepted a resolution in its Synod to recognize Nestorius as a Saint and Church Father. This decision was not however accepted by a minority of Persian Christians who acknowledged a Catholicos at Tigris in northern Mesopotamia as their spiritual head in 629 A.D.

 The Persian connection of the Indian Churches has to be seen in the context of the internal dissension and state persecution of Christians in Persia from the 5th century. A synod of the Persian Church (410 AD) affirmed the faith of Nicea and acknowledged the Metropolitan of Seleucia-Ctesiphon as the Catholicos of the East. Not long after, the Christological controversies of Chalcedon, fuelled by the strains between the Persian and Byzantine empires, swayed the Persian Church to declare itself 'Nestorian' and its head to assume the title of Patriarch of the East (Babylon). From their base in the then flourishing theological school of Nisibis, Nestorian missionaries began moving to India, Central Asia, China and Ethiopia to teach their doctrines - probably associating with the work of St. Thomas the apostle, whom the Persians must have venerated as the founder of their own church.

 By the 7th century, specific references of the Indian Church began to appear in Persian records. The Metropolitan of India and the Metropolitan of China are mentioned in the consecration records of Patriarchs of the east. At one stage, however, the Indian Church was claimed to be in the jurisdiction of the Metropolitan of Far but this issue was settled by Patriarch Sliba Zoha (714-728 AD) who recognized the traditional dignity of the autonomous Metropolitan of India.

 We have evidence that in the 8th century the Indian Church had its Primate known as "The Metropolitan and the Gate of All India' a title adopted presumably under Islamic influence. The Vatican Codex 22, written in Carmagnole in 1301 gives the titles as "The Metropolitan of the Throne of St. Thomas and of the whole Church of the Christians in India."

 There were other developments in the Persian Church of potential import to the Indian Church. A renaissance of the pre-Chalcedon faith began, led by Jacob Baradeus, emphasizing the West Syrian Christological tradition of the One United Nature, influencing the church in Persia as well. Availing the relatively equable political climate following the Arab conquest of Syria and other parts of West Asia, a Maphrianate of the anti-Chalcedonians was established by Mar Marutha, a native Persian, became the first Maphrian (Catholicos) of the East. The jurisdiction of this Catholicos at Tigris extended to 18 Episcopal dioceses in lower Mesopotamia and further east, but significantly, not to India.

The Indian Church maintained its autonomous administration. The Church of Persia had a tradition, which acknowledged autonomy of Churches in its communion abroad. The Church in Kerala continued as an administratively independent community till the 16th century.

 On the life of the Church in India during the first 15 centuries, the balance of historical evidence and the thrust of local tradition point to its basic autonomy sustained by the core of its own faith and culture. It received with the trust and courtesy missionaries, bishops and migrants as they came from whichever eastern Church, Tigris, Babylon, Antioch or Alexandria, but not from the more distant Constantinople or Rome. There were times in this long period when the Christians in India had been without a bishop and were led by an Archdeacon. And requests were sent, sometimes with success, to one or another of the eastern prelates to help restore the episcopate in India. Meanwhile the church in Persia and much of west Asia declined by internal causes and the impact of Islam, affecting both the Nestorian Patriarchate of the East (Babylon) and the Catholicate of the East (Tigris). As will be seen from the later history of the Indian Church, the latter was re-established in India (Kottayam) in 1912 while the former was transplanted to America in 1940.