- Jan 3 Henry II of Bavaria, Bishop of Utrecht (1524-29), Worms (1523-52) and Freising (1541-52), dies at 64
- Jan 11 Johannes Cochlaeus, [Dobeneck], German humanist/theologist, dies
- Jan 22 Edward Seymour, Duke of Somerset, beheaded for treason
- Feb 26 Heinrich Faber, German composer
- Mar 29 Guru Angad Dev, second Sikh Guru, dies at 47
- Apr 14 Laurentius Andreae, [Lars Andersson], Swedish church reformer, dies
- Apr 18 John Leland, English poet and antiquarian, dies at 49
- Apr 21 Petrus Apianus [Peter Apian], German mathematician, astronomer and cartographer, dies at 50
- Jun 10 Alexander Barclay, English poet
- Aug 15 Hermann of Wied, German Catholic archbishop (b. 1477)
- Oct 14 Oswald Myconius, Swiss Protestant reformer (b. 1488)
- Oct 17 Andreas Osiander, Protestant Reformation theologist, dies at 53
- Dec 2 Francis Xavier, Spanish Catholic missionary (b. 1506)
- Dec 3 St Francis Xavier, Jesuit missionary to the East (b. 1506)