- Jan 27 Robrecht de Berghes, prince-bishop of Liege (1557-64), dies
- Mar 17 Alexander Ales [Alesius], Scottish theologian of the school of Augsburg, dies at 64
- May 14 Nicolaus von Amsdorf, German reformation theologist, dies at 81
- Jun 12 Adrianus Turnebus, French classical scholar (b. 1512)
- Jun 17 Ashikaga Yoshiteru, Japanese 13th shōgun of the Ashikaga shogunate (1546-65), dies at 29
- Oct 5 Lodovico Ferrari, Italian mathematician (b. 1522)
- Oct 12 Jean Ribault, French explorer and colonizer (b. 1520)
- Oct 14 Thomas Chaloner, English statesman and poet (b. 1521)
- Oct 22 Jean, Vicomte d'Aguisy Grolier de Servieres, French bibliophile (b. 1479)
- Dec 9 Pius IV [Gianangelo de' Medici], Italian lawyer and Pope (1559-65), dies at 66
- Dec 13 Conrad Gessner, Swiss physician and naturalist, dies at 49
- Dec 18 Benedetto Varchi, Italian humanist and historian (L'Ercolano), dies at 62