- Jan 7 Jacobus de Kerle, French Flemish composer, dies at about 59
- Jan 19 Edmond Auger, French jesuit (under Henri III), dies at about 60
- Feb 5 Gerard de Jode, Flemish publisher and cartographer, dies at about 82
- May 15 Dmitry Ivanovitch, youngest son of Russian Tsar Ivan IV, murdered at 8
- May 17 Jost Amman, Swiss cartoonist, graphic artist and illustrator, dies at 51
- Jun 21 Aloysius Gonzaga, Italian aristocrat and Jesuit saint, dies at 23
- Jul 2 Vincenzo Galilei, Italian composer (b. 1520)
- Jul 18 Jakob Handl, [Petelin], Austrian composer and bandmaster, dies at 40
- Aug 23 Luis de Leon, Spanish scholar and poet, dies at 64
- Sep 12 Richard Grenville, vice-admiral (Roanoke) dies in battle at 49
- Oct 16 Gregory XIV, [Niccolo Sfondrati], Italian Pope, dies at 56
- Nov 20 Christopher Hatton, English politician (b. 1540)
- Dec 14 St. John of the Cross [Juan de Yepes y Álvarez], Spanish Carmelite friar, poet and saint, dies at 49
- Dec 30 Pope Innocent IX [Giovanni Antonio Facchinetti], 230th Catholic pope (1591), dies at 72