- Mar 11 Matthias Flacius, Croatian Protestant reformer (b. 1520)
- Mar 15 Annibale Padovano, Italian composer (b. 1527)
- Mar 24 Yosef Karo, Spanish-born rabbi (b. 1488)
- May 17 Matthew "Nosey" Parker, Archbishop of Canterbury (1559-75), dies at 68
- Jun 2 Pieter Aertsen, [Long Worm], painter, dies at about 65
- Jun 16 Hadrianus Junius [Adriaen de Jonghe], Dutch physician, historian and humanist, dies at 63
- Jul 12 Renée/Renata de France, duchess of Ferara/daughter of Louis XII, dies
- Jul 14 Richard Taverner, English Bible translator
- Sep 17 Heinrich Bullinger, Swiss religious reformer, dies at 71
- Sep 29 Charles de Boisot, water beggar, dies in battle at about 45
- Dec 23 Akiyama Nobutomo, Japanese warrior (hanged) (b. 1531)
- Dec 31 Pierino Belli, Italian soldier and jurist (b. 1502)