He was the youngest child of Francesco Neri, a lawyer of that city, and his wife Lucrezia Soldi, a woman of noble birth, whose family had long served the state.
A characteristic instance of the corruption of the papal court is the fact that Borgia's daughter Lucrezia (see Borgia, LucREZIA) lived with his mistress Giulia, who bore him a daughter Laura in 1492.
The connexion began in 1470, and she bore him many children whom he openly acknowledged as his own: Giovanni, afterwards duke of Gandia (born 1474), Cesare (born 1476), Lucrezia (born 1480), and Goffredo or Giuffre (born 1481 or 1482).
In 1572 he married Francesca Lucrezia daughter of Bartolommeo Giunta, and great-grandchild of the first Giunta, who founded the famous printing house in Venice.
He is known to have painted portraits of two of the king's mistresses, Cecilia Gallerani and Lucrezia Crivelli.
Married Lucrezia Borgia, and continued the war with Venice with success.
His first wife, Ersilia Santa Croce, bore him twelve children, and nine years after her death he married Lucrezia Petroni, a widow with three daughters, by whom he had no offspring.
But there was no end to the Vatican tragedies, and in July the duke of Bisceglie, whose existence was no longer advantageous, was murdered by Cesare's orders; this left Lucrezia free to contract another marriage.
Finally Francesco's wife Lucrezia and his children Giacomo, Bernardo and Beatrice, assisted by a certain Monsignor Guerra, plotted to murder him.
She bore him two sons, Rodrigo, who was once selected to be the husband of Lucrezia Borgia, and Diego, who was the grandfather of the princess of Eboli of the reign of Philip II (see Perez, Antonio.) By another lady of a Valladolid family he had a third son who afterwards emigrated to France.