DISCOVERY OF THE IMAGE OF THE SANTO NINO
Because of Cebuanos suspicion that the Spaniards return has bringing retribution to Magellan's death, another battle broke out. But heavy artilleries and huge cannons forced the natives to flee to the mountain leaving behind their villages burnt to the ground. As Spanish soldiers surveyed the debris of the village, a soldier found an image of the Child Jesus under the pile of ashes unscathed inside a wooden box.

As earlier authenticated entry in the Journal of Pigafetta, clerk in the Magellan expedition, explained the origin of Santo Nino: "On the day Queen Juana was baptized by Father Pedro Valderama, chaplain of that expedition, Pigaffeta himself presented her with the Image." The same Image now lies in the Basilica del Santo Nino and become a favorite destination for millions of pilgrims each year. For four and half centuries now, the Image of Santo Nino continues to make wonders in the lives of many Filipinos. On the third Sunday of each year, in Cebu, millions will flock to the streets in Cebu for a colorful festivity, honoring the Santo Nino and placing the Island and the entire Philippines under His Patronage.

During the last World War, a bomb fell inside the Church but the Image was recovered unscathed. It was one of the numerous miracles and powers attributed to the Holy Image. 
In 1965 the historic Santo Nino Church was renovated for the observance of the Fourth Centenary of the Christianization of the Philippines held in Cebu City. It was during the centennial celebration that the Sacred Congregation of Rites elevated the Santo Nino Church to the rank of Basilica Minore with all the rights and privileges accruing to such title.