- Feb 9 Jeseph Sanalbo, Jewish convert in Rome, burned at stake
- Feb 18 Antonio Francesco Grazzini, Italian writer (b. 1503)
- Mar 4 Bernard Gilpin, English clergyman, "Apostle of the North" (b. 1517)
- Mar 6 Zacharias Ursinus, German theologist (Heidelberger Catechism), dies at 48
- Mar 18 King Magnus of Livonia (b. 1540)
- Jun 6 Nakagawa Kiyohide, Japanese warlord (b. 1556)
- Jun 9 Thomas Radclyffe, 3rd Earl of Sussex, Lord Lieutenant of Ireland
- Jul 6 Edmund Grindal, English bishop of London/archbhp of York, dies at 64
- Sep 9 Humphrey Gilbert, English soldier, explorer and founder of Newfoundland, dies at sea, apparently reading "Utopia", at 43 or 44
- Sep 16 Catherine Jagellion, Polish princess and queen of Sweden as the wife of John III of Sweden, dies at 56
- Oct 30 Pirro Ligorio, Italian architect/painter/archaeologist, dies at 83
- Nov 24 René de Birague, French cardinal and chancellor (b. 1506)
- Dec 31 Thomas Erastus, Swiss physician and theologist, dies at 59