- Feb 9 John Hooper, deprived Bishop of Gloucester, burnt for heresy
- Feb 9 Rowland Taylor, English clergyman, dies at 44
- Mar 23 Julius III [Giovanni Maria Ciocchi del Monte], Counter-Reformation Pope (1550-55), dies at 67
- Mar 27 William Hunter, Protestant martyr
- Apr 12 Joanna of Castile (Joanna the mad), wife of Philip I of Castile dies at 75
- May 1 Marcellus II [Marcello Cervini], Italian humanist and Pope (1555, 22 days), dies at 53
- May 25 Gemma Frisius [Jemme Reinerszoon], Frisian physician, mathematician and instrument maker (created globe), dies at 46
- May 25 Henry II of Navarre (b. 1503)
- Jun 7 Maarten van Rossum, Dutch army leader, dies at about 76
- Jun 23 Pedro Mascarenhas, Portuguese explorer (b. 1470)
- Aug 8 Oronce Finé, French mathematician (b. 1494)
- Sep 8 Thomas Villanova, Spanish saint/archbishop of Valencia, dies
- Oct 7 Louis of Praet, Habsburg diplomat (b. 1488)
- Oct 9 Justus Jonas, German Protestant theologian and reformer, dies at 62
- Oct 16 Hugh Latimer, English bishop and royal chaplain, burned at the stake as one of the Oxford Martyrs at 80
- Oct 16 Nicholas Ridley, English theologist/bishop of Rochester, burned at the stake as an Oxford martyr
- Nov 12 Stephen Gardiner, English bishop of Winchester, dies at about 65
- Nov 21 Georg Agricola [Bauer], German mineralogist (zinc), dies at 61
- Nov 24 French Vervoort, Flemish mystic (Bruylocht Cleedt), dies at about 65