History of the church
In 1521, the Portuguese in Goa and Bombay-Bassein sent missionaries to Madras (Chennai) seeking the tomb of the famed Thomas the Apostle, which had become neglected or maintained nominally by Muslims, and they decided to rebuild the shrine over the tomb of the apostle. With the order and funding of King John III of Portugal they started building the church. In 1523, the structure was consecrated as a church, and Portuguese Padroado priests resumed the daily celebration of Liturgy (Holy Mass) at the site.
In 1545, St Francis Xavier visited the shrine and lived for about one year in the presbytery of the Santhome Church before he left for his mission in Ilha Formosa, the Portuguese name for the island of Taiwan. When he lived in Santhome Church he regularly prayed in front of a statue of the Virgin Mother Mary and celebrated Holy Mass; he also prayed regularly at the tomb bearing the relics of St Thomas.