His godfather was Francesco Borgia, Archbishop of Cosenza, while Cardinal Carafa of Naples performed the rite in the Sistine Chapel.

The child was very quiet, but as soon as he was in Orsini's arms, long time enemies of the House of Borgia suddenly reconciled, Rodrigo began to cry and would not stop until he was given back to his mother.

After Alexander VI's death in 1503, the enemies of the Pope locked Rodrigo in Castel Sant'Angelo with the rest of the Borgia family.

Lucrezia arranged a discharge of their children by correspondences and alliances and requested that Rodrigo be raised by the family of Alfonso of Aragon.

Rodrigo lived with his father's sister Sancha of Aragon until her death in 1506, then he grew up with Isabella of Naples, Duchess of Bari.