The church of Virgin Mary was located close to the Harbor Baths of the ancient city of Ephesus. It was a 260 m long basilica used initially as a medical centre; a small chapel was added to it in the 10th century AD. It could be accessed through an atrium which had been paved with marble slabs. Crosses and metal rosettes adorned its walls and a baptism pool had been constructed to the north of the church.

The Council of Ephesus held meetings here in 431 AD discussing the role of Saint Mary as the Mother of God. They agreed at least on the fact that she came to Ephesus accompanied by Saint John and that she died there. It was the first one devoted to the Virgin Mary and the Council of Ephesus and the Synod declared that church as the centre of Christianity in 449 AD.