São Roque's collection of 16th and 17th century reliquaries are now exhibited in the two reliquary altars (Holy Martyrs [male] on the left or Gospel side, and Holy Martyrs [female] on the right or Epistle side) flanking the chancel as well as being partially integrated into the decoration of the Chapels of Our Lady of the Doctrine, Of the Holy Sacrament, and of Our Lady of Piety. They are worthy of special mention not only for their symbolic, spiritual and artistic value, but also because of their close historical and iconographic connections to the Society of Jesus.
Francisco de Borja (St. Francis Borgia, 1510-72), fourth Duke of Gandía and father of the relic collector and donor D. João de Borja, took his Jesuit vows at the somewhat late age of 41. He had married D. Leonor de Castro, the mother of D. João, in 1529, but she died in 1546. D. João served at the first mass said by his father in the palace of D. Martim Garcia de Oñaz y Loyola, brother of Ignatius Loyola, the founder of the Society of Jesus. St. Francisco de Borja preached at St. Roch's in 1553 in the presence of King John Ill when the Society took possession of the original shrine. In 1565 he became the third Superior General of the order and as such was personally interested in the construction of the Church of São Roque and the attached Jesuit residence.
D. João (or Juan) de Borja (1533-1606) was married twice, first to Lorenza de Oñaz (grand-daughter of Ignatius Loyola's brother), and later to D." Francisca of Aragón y Barreto (of Portuguese origin). He followed the construction in São Roque's Church closely. Later he was sent as ambassador of Philip Il of Spain to the Imperial court of Rudolf Il of Saxony. D. João was able to assemble a first rate collection of relics from, among other places, Rome, Hungary, Bohemia and Cologne which he brought back to the Escorial where he drew up a deed of gift to São Roque's Church in 1587. In return the grateful Jesuits decided to allow the donors — D. João and his wife as well as their descendants — to be buried in the main chapel'.
The reliquaries at São Roque, most of them from D. João de Borja, are of different shapes, generally depending on the relic they house: arms, male and female torsos, urns, ostensories, chests. The majority, with their pontifical certificates and letters, are of great historical and artistic value. The glass cases holding the reliquaries were created in 1898 at the time of the commemoration of the fourth centenary of the creation of the Charity House of Lisbon.