According to apocryphal records, Christianity in India and in Pakistan (included prior to the Partition) commenced in 52 AD, with the arrival of Thomas the Apostle in Kodungallur (Cranganore). Subsequently, the Christians of the Malabar region, known as St Thomas Christians established close ties with the Levantine Christians of the Near East. They eventually coalesced into the Church of the East led by the Catholicos-Patriarch of Seleucia-Ctesiphon.

The Church of the East was often separated from the other ancient churches due to its presence in the Assyrian-Parthian Empire, an ancient rival of the (Byzantine) Greek and (Latin) Roman Empires. When Archbishop Nestorius of Constantinople was declared a heretic by the Council of Ephesus, the Church of the East refused to acknowledge his deposition because he held the same christological position. Later, the "anaphora of Mar Nestorius" came to be used by Church of the East, which for this reason has been pejoratively labelled the "Nestorian Church" by its theological opponents.

When the Portuguese Inquisition in Goa and Bombay was established in the 16th century, they opposed the East Syriac rite of Christian worship in what was Portuguese Cochin. After the schism of 1552, a section of the Church of the East became part of the Chaldean Catholic Church, both the Assyrian and Chaldean patriarchates intermittently attempted to regain their following in the Indian subcontinent, by sending their prelates to the Malabarese Christians. The Vatican supported the claim of the bishop from the Chaldean Church of Ctesiphon. But the Portugal-sponsored Synod of Diamper in 1599, overseen by Aleixo de Menezes, the Portuguese Archbishop of Goa, replaced the East Syriac bishop of St Thomas Christians and placed them under the Portuguese Padroado-backed bishop. After that any attempts of Thomas Christians to contact bishops, even Chaldean Catholic ones in the Middle East were foiled.

Mar John, Metropolitan of India (1122 AD)

In 1122, Mar John, Metropolitan-designate of India, with his suffragans went to Constantinople, thence to Rome, and received the pallium from Pope Callixtus II.The realm of Prester John, Silverberg, pp. 29–34. He related to the Pope and the cardinals the miracles that were wrought at the tomb of St. Thomas at Mylapore.Raulin, op. cit., pp. 435-436. Counto. Asia Lisbonne, 1788, Dec. XII, p. 288. These visits, apparently from the Saint Thomas Christians of India, cannot be confirmed, as evidence of both is only available from secondary sources.Halsall, Paul (1997). Otto of Freising: The Legend of Prester John . Internet Medieval Sourcebook. Retrieved 20 June 2005.Silverberg, pp. 3–7Bowden, p. 177 Later, a letter surfaced during the 1160s claiming to be from Prester John. There were over one hundred different versions of the letter published over the next few centuries. Most often, the letter was addressed to Emanuel I, the Byzantine Emperor of Rome, though some were addressed to the Pope or the King of France.

Historian Meir Bar-Ilan notes that a 20th-century collection of Hebrew Prester John Letters, edited by Ullendorff and Beckingham (1982) "present[s] a Latin text with its Hebrew translation (and an English text where the Latin is missing) as follows": Citing: "The Hebrew letters of Prester John were printed in Constantinople 1519, and later in": Neubauer, A. (1888). "Collections on the Lost Ten Tribes and the Children of Moses" Qobes al Yad, vol. IX, pp. 1–74; ; and Ullendorff, E.; Beckingham, C. F. (1982). The Hebrew Letters of Prester John. Oxford: Oxford University Press.

Bar-Ilan concludes that evidence from the Hebrew Letters "shows that Prester John lived in India; or to be more precise, in Malabar (southern India)".

Mar Ya'qob Metropolitan of India and Patriarch Yahballaha III

At the beginning of the fourteenth century, the Indian church was again dependent upon the Church of the East. The dating formula in the colophon to a manuscript copied in June 1301 in the church of Mar Quriaqos in Cranganore mentions Patriarch Yahballaha III (whom it calls Yahballaha V) and Metropolitan Yaqob of India. Cranganore, described in this manuscript as "the royal city", was doubtless the metropolitan seat of India at this time.MS Vat Syr 22;

In the 1320s, the anonymous biographer of the patriarch Yahballaha III and his friend Rabban Bar Sauma praised the achievement of the Church of the East in converting "the Indians, Chinese and Turks".Wallis Budge, The Monks of Kublai Khan, 122–123 India was listed as one of the Church of the East's "provinces of the exterior" by the historian Din ‘Amr in 1348.

Yahballaha maintained contacts with the Byzantine Empire and with Latin Christendom. In 1287, when Abaqa Khan's son and successor Arghun Khan sought an ambassador for an important mission to Europe, Yaballaha recommended his former teacher Rabban Bar Sauma, who held the position of Visitor-general. Arghun agreed, and Bar Sauma made a historic journey through Europe; meeting with the Pope and many monarchs; and bringing gifts, letters, and European ambassadors with him on his return. Via Rabban Sauma, Yahballaha received a ring from the Pope's finger, and a papal bull which recognized Yahballaha as the patriarch of all the eastern Christians.Phillips, p. 123

In May 1304, Yahballaha made profession of the Catholic faith in a letter addressed to Pope Benedict XI. But a union with Rome was blocked by his Nestorian bishops.

Udayamperoor (known as Diamper in Portuguese), the capital of this kingdom, was the venue of the famous Synod of Diamper of 1599. It was held in the All Saints Church there. The venue was apparently chosen on account of the place having been the capital of a Christian principality.

Synod of Diamper and suppression of East Syriac jurisdiction in India

In 1552, there was a schism in the Church of the East and a faction led by Mar Yohannan Sulaqa declared allegiance to Rome. When, on 6 April 1553, Pope Julius III confirmed Yohannan Sulaqa as Chaldean Patriarch, the Pope said that the discipline and liturgy of the Chaldeans had already been approved by his predecessors, Nicholas I (858–867), Leo X (1513–1521), and Clement VII (1523–1534). Thus, parallel to the "traditionalist" (often referred as Nestorian) Patriarchate, the "Chaldean" Patriarchate in communion with Rome came into existence and both traditionalist and Chaldean factions began sending their own bishops to Malabar.

When the Portuguese arrived in Malabar, they assumed that the four bishops present were Nestorian. Their report of 1504, addressed to the Chaldean Patriarch, their being startled by the absence of images and by the use of leavened bread; but this was in accordance with Chaldean usage. The Christians paid the expenses of the Papal delegate Marignoli.Father Nidhiry: A History of His Times by Prof. Abraham Nidhiry

The Synod of Diamper of 1599 marked the formal subjugation of the Malabar Syriac Christian community to the Latin Church. It implemented various liturgical and structural reforms in the Indian Church. The diocese of Angamaly, which was now formally placed under the Portuguese Padroado and made suffragan to the archdiocese of Goa. The east syriac bishop was then removed from jurisdiction in India and replaced by a Latin bishop; the East Syriac liturgy of Addai and Mari was “purified from error”; and Latin vestments, rituals, and customs were introduced to replace the ancient traditions.

Accounts of foreign missionaries

Francis Xavier wrote a letter dated 26 January 1549, from Cochin to king John III of Portugal, in which he declared that:

In that same year, Francis Xavier also wrote to his Jesuit colleague and Provincial of Portugal, Fr. Simon Rodrigues, giving him the following description:

This attitude of St. Francis Xavier, and of the Franciscans before him, does not reflect any of the animosity and intolerance that kept creeping in with the spread of the Tridentine spirit of the Counter-Reformation, which tended to foster a uniformity of belief and practice. It is possible to follow the lines of argument of young Portuguese historians, such as Joéo Paulo Oliveira e Cosca, yet such arguments seem to discount the Portuguese cultural nationalism in their colonial expansion and the treatment of the natives. Documents recently found in the Portuguese national archives help to confirm a greater openness or pragmatism in the first half of the 16th century.Arquivio Nacional torre do Tombo Lisbo:Nucleo Antigo N 875 contains a summary of letters from india written in 1525 and also the kings replay to it :Cf.OLIVERIA E COSTA, Portuguese, Apendice Documental 170-178

Malankara-Persian ecclesiastical relations Several historical evidences shed light on a significant Malankara–Persian ecclesiastical relationship that spanned centuries. While an ecclesiastical relationship existed between the Saint Thomas Christians of India and the Church in Sassanid Empire (Church of the East) in the earlier centuries, closer ecclesiastical ties developed as early as seventh century, when India became an ecclesiastical province of the Church of the East, albeit restricted to matters of purely ecclesiastical nature such as ordination of priests, and not involved in matters of temporal administration. This relationship endured until the Portuguese protectorate of Cochin of Malabar came to be in 16th century, and the Cape Route, a Portuguese discovery of a sea route to India. The Christians who came under the two ancient yet distinct lineages of Malankara and Persia had one factor in common: their Saint Thomas heritage. The Church of the East shared communion with the Great Church (Catholicism, Eastern Orthodoxy and Oriental Orthodoxy) until the Council of Ephesus in the 5th century, separating primarily over differences in Christology.

The Saint Thomas Christians of India came in contact with Portuguese Latin Catholic missionaries only in the 16th century. Later, after the Oath of Koonan Cross (meaning "leaning cross") in 1653, the Saint Thomas Christians came in touch with the Syriac Orthodox Church.

Though claims have been made that the Saint Thomas Christians of Malankara had close interactions with the Roman Catholic Church and Syriac Orthodox Church before the 16th century, these assertions lack proof.

Early references

The celebrated Church historian Eusebius has mentioned in his work that the Alexandrian scholar Pantenus:nl:Pantenus had seen Christians during his visit to India between 180 A. D. and 190 A. D. This account of Eusebius has later been quoted by several historians. According to Eusebius, Pantenus saw people reading the Gospel according to Mathew in Hebrew. Based on this reference by Eusebius, Jerome has recorded the existence of Christians in India during the early centuries of Christian Era. In addition to this, Jerome mentions that Pantenus held debates with Brahmins and philosophers in India.

The evangelization of India is mentioned in a number of ancient works, including the book Acts of Judas Thomas written in Edessa around 180 A. D. in Syriac language, and Didascalia (meaning teachings of the Apostles) written around 250 A. D. Historians have often remarked that the Persians might have received this tradition about the Church in India from India itself.

The Chronicle of Seert is a historical document compiled in the Middle Ages. In this Chronicle, the Church in India is mentioned along with the history of Persian Church and the Patriarchs (Catholicoi) of Babylon. It also states that during the reigns of Shahlufa and Papa bar Aggai as the heads of Persian Church, the Persian bishop David of Basra preached the Gospel in India. Some historians' records regarding the participation of Bishop John representing Persia and India as the Bishop of all of Persia and Greater India in the first Ecumenical Council of Nicaea in 325 A. D. remains a matter of contention among historians.