In 1619, the residents of Old Goa were surprised to see several crimson flags fluttering in the air near a teakwood cross set on a rock on a hill. On the following morning, from a distance, they saw a human figure nailed on the cross, a halo of light encircling him. When they reached the spot, the vision had vanished. It was to appear again, its head uplifted, the body covered with wounds and stained with blood and a crown of thorns round the head. A canonical investigation reported that many people had been cured by simply touching the cross. When the cross was removed from the church to a new one (the Church of the Miraculous Cross, specially built for it on the hill where the vision had first appeared), it was found to have grown in size. The entrance had to be widened before it could pass through. Its present length is just over 20 ft.

In the grounds of St Pauls College stands the St Francis Xaviers Chapel where Francis Xavier used to pray. On the right side of the road leading to the chapel is an arched well (a typical Portuguese-Oriental construction). The clean of heart, it is said, will see burning candles when they look into the well. At the foot of this chapel, Goencho Baab, as he is known, planted a jackfruit tree. Its bark was said to possess the power to heal various illnesses.