- Feb 13 Gian Paolo Lomazzo, Italian painter and poet (Trattato), dies at 61
- Feb 15 Jose the Acosta, Spanish missionary (Peru), dies at 59(?)
- Feb 17 Giordano Bruno, Italian friar and scholar, advocate of Copernican theory, burned at the stake at 51 or 52
- Aug 2 Arent van Dorp, Dutch governor of East-Zealand, dies at about 70
- Sep 1 Tadeáš Hájek, Czech physician (b. 1525)
- Sep 10 John Bruhesius [Bruhesen], bishop of Groningen, dies
- Oct 12 Luis Molina, Spanish Jesuit priest (De liberi arbitrii cum gratiae donis), dies at 65
- Oct 21 Toda Katsushige, Japanese warlord (b. 1557)
- Nov 3 Richard Hooker, English theologian (b. 1554)
- Nov 8 Natsuka Masaie, Japanese warlord (b. 1562)
- Nov 12 Andreas of Austrian, Land Guardian of Netherlands (1598-1600), dies at 42