Born in Naples, Carafa was the yougher son in a powerful noble family. He became a soldier and for seventeen years took part in the bloody wars which ravaged Italy, first on the side of the Habsburg imperial armies, afterwards with French troops.
His uncle, Gian Piero Carafa was elected pope, with the name of Paul VI, and made Carlo a cardinal in 1555. Carlo had in his hands the Government of the Pontificial State; he participated in diplomatic games where the interest of his family were superior for Carafa than the interests of the pope's state. As the pro-French opponents of Carlo and Giovanni Carafa, the nephews of the upright and moralistic Paul IV, the scandalous conduct of the two men was violently denounced to the pontiff.
For instance the cardinal Charles de Lorraine asked the French ambassador in Rome to report to the pope scandals concerning his nephews. In his letter he stated that the courtiers had been scandalized by what they had witnessed, "and among the culprits were openly numbered, those who were closest in blood relations to our Holy Father the pope" had engaged in "that sin so loathsome in which there is no longer a distinction between the male and the female sex."
These rumors cannot be explained away as political slander. Already the poet Joachim du Bellay who was then in Rome, wrote a sonnet mentioning one Ascanio as the beloved of Carlo Carafa. At first the pope refused to believe the numerous and varied accusations, but he was finally convinced of their veracity; furious with his nephews he deprived them of their positions and exiled them.
With the death of Paul IV, who already limited a part of his power, he was imprisoned and judged by the new pope Pius IV for a lenghty series of crimes ranging from homicide to heresy, among which was also sodomy. Carlo was condamned and executed.