- Jan 3 Joachim II Hector, elector (Brandenburg), dies at 65
- Jan 9 Nicolas Durand de Villegaignon, French naval officer (b. 1510)
- Feb 12 Nicholas Throckmorton, English diplomat and politician (b. 1515)
- Feb 14 Benvenuto Cellini, Italian sculptor/writer (Perseus), dies at 70
- Feb 14 Odet de Coligny, Cardinal of Châtillon and count of Beauvais, dies at 53
- Apr 6 John Hamilton, Scottish prelate and politician
- Jun 1 John Story, English Catholic martyr, executed at Tyburn by being hung, drawn and quartered
- Jul 15 Shimazu Takahisa, Japanese samurai and warlord (b. 1514)
- Jul 17 Georg Fabricius, German poet, historian and archaeologist, dies at 55
- Sep 4 Earl of Lennox, regent of Scotland, murdered
- Sep 23 John Jewel, English bishop, dies at 49
- Oct 4 Claude Togniel d'Espence, French theologist (Sorbonne), dies at 60
- Oct 7 Müezzinzade Ali Pasha, Turkish fleet commander, dies in the Battle of Lepanto
- Oct 7 Dorothea of Saxe-Lauenburg, Queen of Denmark and Norway, dies at 60
- Nov 24 Jan Blahoslav, Czech bishop, dies at 48