- Pilgrimage of Saint Gregory the Great. An annual pilgrimage was initiated by Bishop Cubelles in 1543 to pray for the intentions of Pope Paul III who was endeavouring to bring together Christian rulers in Europe for an the Ecumenical Council at a time when the church was undergoing significant division and was in need of reformation. The pilgrimage started at dawn from the Cathedral in Mdina and ended a the church of St. Gregory’s in Zejtun. Others attribute the procession to earlier dates (such as 1120) as thanksgiving following a failed attempt by Arabs to re-capture the island or a failed Turkish attack in 1452, sparing from a devastating plague in 1519. These and other events may all have been reasons for thanksgiving attributed to the pilgrimage which – later in 1543 – was firmly established as an annual event by Bishop Cubelles as an intercessory pilgrimage for Christian Unity.
- Saint Paul’s Grotto, Rabat. The grotto where Saint Paul is said to have been imprisoned during his 3 months’ stay in Malta. The Spanish hermit Don Juan Benegas de Cordoba acquired the land above the grotto in the 16th century with the intention of attracting pilgrimages to this shrine. Grandmaster Alof de Wignacourt built a chapel dedicated to St. Publius above the crypt and an adjacent college of chaplains to minister to the pilgrims. Visitors to the grotto include Pope Alexander VII, Lord Nelson, Pope Paul John II and Pope Benedict XVI.
Malta also has other, older or more recent shrines and pilgrimage sites but of a more local nature.