- Jan 4 Hosokawa Ujitsuna, Japanese military commander (b. 1514)
Michelangelo
Feb 18 Michelangelo, Italian sculptor, painter, architect and poet of the High Renaissance (David, Ceiling of the Sistine Chapel), dies at 88
Michelangelo
- May 2 Cardinal Rodolfo Pio da Carpi, Italian humanist (b. 1500)
John Calvin
May 27 John Calvin [Jehan Cauvin], Protestant religious reformer and theologian (Calvinism), dies at 54 (b. 1509)
John Calvin
- Jun 2 Gellius Faber, [Jelle Smit], Fries theologist, dies
- Jul 25 Ferdinand I, Holy Roman Emperor (1558-64), dies at 61
- Oct 2 Andreas Vesalius [Andries van Wesel], Flemish-Netherlandish physician and anatomist (De humani corporis fabrica), dies after being shipwrecked at 49
- Oct 3 Christophorus Fabritius, [Christoffel Smit], calvinist vicar, burned
- Oct 4 Pietro P Vergerio, Italian theologist/bishop of Croatia, dies
- Oct 5 Pierre de Manchicourt, Flemish composer
- Oct 18 Johannes Acronius Frisius, German physician and mathematician (b. 1520)