Philip, following the directions of Charles V, sent Don John to the [[Complutense University]] in the company of Don Carlos and [[...|Alessandro Farnese]], Prince of [[Parma]] and son of Charles V's other acknowledged illegitimate child, [[Margaret of Parma|Margaret of Austria, Duchess of Parma]] (1522–86). This was meant to be a preparation for Don John his ecclesiastical career. At [[Alcalá]] in 1562, Carlos suffered a fractured skull that had a deleterious effect on his personality. In 1565, Farnese left to be married in Brussels, where his mother was [[Regent]] of the Low Countries. From [[...|Farnese]], Don John is said to have learned womanizing and, in time, acknowledged two illegitimate daughters, one in Spain, the other in Naples.refref
The former, Ana de Austria (1568 – 1610), daughter of Ana de Mendoza y Lacerda, 1st Princess of [[Melito]] and 1st Duchess of , became an [[abbess]]; the latter, Juana de Austria (11 September 1573 – 7 February 1630), after years in a convent, married an Italian nobleman, Francesco Branciforte, Prince of [[Pietraperzia]] (c. 1575 – 1622) in 1603. They had a daughter Margherita Branciforte, Princess of [[Butera, Italy|]] (d. 24 January 1659, Rome), who married Federico Colonna (1601 – 25 September 1641) and had one son Antonio Colonna, Prince of [[Pietrapersia]] (1619 – 1623).
Don John allegedly sired an illegitimate son from a liaison with Zenobia Sarotosia while in Italy. The child is said to have died at childbirth (c. 1574), although it was rumoured that Philip had a hand in the unfortunate death of the child.refref