- Jan 3 Bartholomeus Latomus [Steinmetz], Flemish archbishop of Trier, dies
- Jan 8 Philibert de l'Orme, French royal architect (Château de Chenonceau), dies at about 55
- Mar 12 Jacob van den Eynden, Grand Pensionary of Holland, dies
- Jul 3 Antonio Paleario, Italian humanist, executed by inquisition at 67
- Jul 25 Ivan Viskovatyi Russian Foreign Minister, executed on orders of Ivan the Terrible
- Sep 11 Johannes Brenz, German theologist (Dutch Brentians), dies at 71
- Oct 1 Frans Floris, Flemish painter (b. 1520)
- Oct 14 Floris van Montmorency, baron of Montigny, dies at 43
- Oct 16 Baron van Montigny, Dutch earl of Horne, murdered
- Oct 18 Manoel da Nóbrega, Portuguese Jesuit in Brazil (b. 1517)
- Oct 20 João de Barros, Portuguese historian (b. 1496)
- Nov 27 Jacopo Sansovino, Italian sculptor and architect (b. 1486)
- Dec 5 Johan Friis, Danish statesman (Chancellor of Denmark, helped establish Lutheranism), dies at 76