Charles V had an illegitimate daughter in 1522 with a woman called Johanna van der Gheenst, who was of much lower rank (some sources indicate she was basically a servant). Margaret was married off to advance the Emperor's Italian policy and strengthen his relationship with the Papacy: first to Alessandro de Medici, Duke of Florence (purported nephew, and suspected bastard son, of Pope Clement VII), who was assassinated in 1537, and subsequently to Ottavio Farnese, grandson of Pope Alexander III. In Italy she was known as "Madama," in English she is more usually called Margaret of Parma.In between marriages, she was sought eagerly by Cosimo de Medici, who hoped to replace his cousin Alessandro, but the Emperor denied him his daughter (while making him Grand Duke of Tuscany). Later, she was made Regent of the Netherlands by her half-brother Philip but her reign was turbulent and unsuccessful, as the Low Countries resisted Spanish rule and religious coercion. Some historians have commented that Margaret had a serious handicap in being unable to speak Flemish with her fellow countrymen; her mother had been a Flemish woman, but the infant was taken from her immediately and educated only in French, Italian, Spanish and Latin.She was a stout, large woman, resembling her father in his middle age, and masculine in her appearance. A new book called Lesbians in Early Modern Spain discusses Margaret's possibly transgressive sexuality in the context of Renaissance culture; she had apparently a very close relationship with an attendant called Laudamia.Margaret had twins by her second husband; the survivor of the set, Alessandro Farnese, inherited the Duchy of Parma. A very talented military commander, he was an important component of Philip II's foreign policy in the Netherlands and a critical element of the Armada invasion (his role was to embark the Spanish army from Flanders to invade England). You may recall Queen Elizabeth's speech at Tilbury, "I think foul scorn that Spain, or Parma, or any prince of Europe should dare to invade the corners of my realm ..."After the Empress died, Charles V had a liaison with a Regensburg woman, Barbara Blomberg. The result was a son in 1545, who grew up to be Don John of Austria. Don John and a papally backed Venetian-Spanish "Holy League" coalition defeated the Turks in a major naval battle off Lepanto in 1571; even Queen Elizabeth ordered the bells to be rung to celebrate the victory.Don John, despite his looks, charm and ability, had a rather sad life that came to nothing, owing to the jealousy of his brother Philip II, who was also rumored to have poisoned him. Like Margaret, John was also sent to the Netherlands, and failed to quiet the provinces, only incurring the enmity of the Duke of Alva and the continued opposition of William of Orange. Don John was mooted as a bridegroom for Mary Queen of Scots in her captivity, but like many other schemes associated with him, it came to nothing. He died in 1578, and I think left an illegitimate daughter.
Don John was born late in the Emperor's life and his mother, unmarried during her affair with the Emperor, had a bad reputation. Consequently he was brought up secretly; Philip II was only told of his existence after the Emperor's death in 1558. The Emperor seems to have wanted Don John to enter the Church and consequently gave him no title. Philip was generous enough to recognize his brother's indifference to a clerical career and his innate abilities, and allowed him to embark on a military career. I don't think he ever gave him a formal rank or title other than "Don John of Austria." Some sources call him "Duke of Austria" but I think this may be a utilization of the German practice, whereby the children of a German count or duke are also counts and dukes.
Brantome briefly mentions an illegitimate son of Francis I, Nicholas d'Estouteville, seigneur de Villeconnin (also rendered Villecouvrin) in the context of a long discussion of women who demand pensions or support for their bastards; d'Estouteville was apparently given 200,000 ecus. Desmond Seward picked this up and mentioned it in his biography of Francis, but the king's most recent biographer in English, R.J. Knecht, makes no mention of Estouteville or any other illegitimate child of Francis. There is also apparently a French source that claims Louis de Saint-Gelais as a natural son of Francis, but there are others that simply describe Saint-Gelais as the legitimate son of his legal father, Alexandre de Saint-Gelais. The Saint-Gelais were closely associated with Francis' father, and Louis de Saint-Gelais appears to have been an intimate of Catherine de Medici, but I can't find out what the evidence is for calling him a son of Francis I.Despite two wives, two official mistresses, and innumerable casual ladyfriends, Francis appears only to have had the seven children by his first wife, if we exclude the putative bastards above (who were certainly not given important titles or formally acknowledged during the lifetime of the king). It has been suggested that the childlessness of his second wife, Eleanor of Austria, was due to a deliberate policy by the king not to increase the influence of the sister of his enemy, the Emperor, or rear a half-Habsburg family that might challenge, with the Empire behind them, his recognized heirs. But Francis' sister Marguerite also related a naughty story, claiming that Francis avoided Eleanor because she was "too hot in bed and wanteth too much to be embraced."He might have become infertile after his first marriage. The apothecary records show that he was taking medicines used to treat syphilis, and while syphilis might not have rendered him sterile, it could point to him having other venereal diseases - which he might have passed along in turn to his female companions, compromising their fertility.
Charles V also had two other illegitimate daughters, the first one called Juana was by an unknown mother, borned in Castile in 1523 and died young in 1530. The other one, called Theodea or Theodora, was born closely after Juana in Bologna (Italy) circa 1523. The mother was possibly a woman called Ursulina de la Peña. Theodea or Theodora was grown up in Bolognia were she married circa 1536 Sinibaldo de Copeschi, a city noble man, dying after 1562. Don John, the illegitimate child by Barbara Blomberg (her real surname was Plumberger) actually had two illegitimate daughters. The first one, Ana, was born in 1568 and died circa 1610. She was abbess of Burgos. Ana´s mother was Maria Ana de Mendoza, illegitimate daughter herself of Diego Hurtado de Mendoza, prince of Melito and father of the famous princess of Evoli. John´s second illegetimate daughter, Giovanna (aka Juana) was born in 1573 at Naples, married at Palermo in 1603 to Francesco Branciforte, prince of Pietrapersia, and died in 1630. Giovanna´s mother was a noble neapolitan woman called Diana Falangola (afterwards married to Pompeo Pieri Piccolomini, of the Lords of Sticciano).
Felipe Fernandez Armesto alleges in his book on Charles V that the Emperor had an affair with his widowed step-grandmother, Queen Germaine de Foix, with the union producing an illegimate daughter, Dona Isabel. I haven't been able to find out much information on this personage and the reported evidence seems to me as if it might be construed differently. However, I haven't researched this question and the references are very sparse. Still, Henry VIII's alleged fathering of two children on Anne Boleyn's sister seems a rather minor incestuous affair compared to this case, if it's true.
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