The present structure dates back to 1523 AD, when it was built by the Portuguese over the tomb of Thomas the Apostle.

In 1521, the Portuguese in Goa and Bombay-Bassein sent missionaries to Madras (now Chennai) in search of the tomb of Thomas the Apostle, who by local tradition had come to South Asia to preach the Gospel and spread the teachings of Jesus Christ.

In 1545, 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 (Taiwan).

Pope Pius XII honoured this cathedral church, elevating it to the dignity and rank of a minor basilica in 1956.

The statue in the main altar represents "Thomas the Apostle as priest and Jesus Christ as king".

It is installed at the left side of the church altar and is referred to as Our Lady of Mylapore or, locally, Mylai Matha.

Worshippers show devotion to Mylai Matha on the second Saturday of the month, with special prayers, procession, rosary and benediction in the evening.