- Jan 21 John Ligarius, German theologist/prime minister, dies at 66
Francis Drake (c. 1540-1596)
Jan 28 English pirate, Admiral and Governor of Newfoundland (Porto Bello West Indies), dies of dysentery at 50
- Feb 17 Friedrich Sylburg, German classical scholar (b. 1536)
- Feb 19 Blaise de Vigenère, French cryptographer, dies at 72
- Mar 23 Henry Unton, English diplomat
- May 6 Giaches de Wert, Franco-Flemish composer of madrigals, dies at approximately 60
- May 27 Tibaldi II, Italian painter/sculptor/architect, dies
- Jul 29 Jacobus Latomus, Flemish poet (Psalms/Jeremias), dies at about 84
- Aug 11 Hamnet Shakespeare, son of William Shakespeare (b. 1585)
- Sep 9 Anna Jagiellon, Queen of Poland and Grand Duchess of Lithuania (1575-87), dies at 72
- Sep 13 Pieter Dirkszoon Keyser, Dutch astronomer and navigator (Java)
- Sep 15 Leonhard Rauwolf, German physician and botanist (b. 1535 or 1540)
- Oct 3 Florent Chrestien, French writer (b. 1541)
- Nov 1 Pierre Pithou, French lawyer and scholar (Les Libertés de l’église gallicane), dies at 57
- Nov 10 Peter Wentworth, English Puritan politician (b. 1530)
- Dec 8 Luis de Carabajal, 1st Jewish author in America, executed in Mexico
- Dec 27 Pietro Pontio, Italian composer (Ragionamento di Musica), dies at 64