Christianity in Goa has pre-Portuguese roots, according to a few scholars such as H.O. Mascarenhas and Jose Cosme Costa. These roots are probably the same as those of the Saint Thomas Christians or Nasranis of Kerala.
H.O. Mascarenhas proposed the theory of pre-Portuguese Christianity in Goa. In an interview, Mascarenhas reports hearing from his grandmother about pre-Portuguese Christianity in Goa. His grandmother was from Aldona, Goa, where the parish church is dedicated to St. Thomas. She spoke of the equal-armed crosses (still found all over Goa today) without the image of Jesus which is common among Saint Thomas Christians. Mascarenhas himself recalls that the Hindus in Goa used to celebrate 3 July (the feast of Thomas the Apostle) as Dukrana, which he later realized as somehow similar to the Syriac 'Dukrana' which is the feast of the martyrdom of Thomas. He also reports the existence of Christian and Hindu 'Thomses' in Kalyanpuram near Mangalore, probably people who fled or migrated from Goa. Again, in a letter from Goa dated 20 September 1542, four months after his arrival, Francis Xavier writes that the people of the land were greatly devoted to St. Thomas. According to Mascarenhas, this could not have come from the Portuguese, who had no great devotion to Thomas the Apostle. Yet another argument is that Francis Xavier suggests that the Pope be petitioned for a plenary indulgence for the feast of St. Thomas. However, at that time the Latin church celebrated the feast of St. Thomas on 21 December and not on 3 July, which was the date on which Syrian Christians celebrated the feat. Mascarenhas suggests therefore that Francis Xavier had witnessed the celebration of the feast on 3 July; he could not have witnessed a celebration on 21 December, since he had just arrived in Goa in May 1542.
Jose Cosme Costa reports that Mascarenhas even proposed that there were Christian temples dedicated to the persons of the Trinity: Abanath / Bhutnath (Father Lord), Ravalnath (from Rabboni - Rabulna - Rabulnath) / Bhai rav (Brother Lord), and Atman / Bhavka Devta, Santeri, Ajadevi (Spirit).
An archaeological discovery (on 27 April 2001 by Jose Cosme Costa, SFX) of a 'Thomas Cross' hidden in a smallish monument, surmounted by a Latin Cross, near the old Goa harbour (now on the Zuari river, near Agaçaim) lends support to this thesis. Cosme Jose Costa, historian at Pilar, Goa, has dedicated a recent work to the implications of this discovery: Apostolic Christianity in Goa and in the West Coast. The Cross bears an inscription in Pahlavi, which, Costa reports, was the liturgical language of the church associated with the Metropolitan of Fars.