January 6 – Shane O'Neill of Tyrone pleads his cause at the Palace of Whitehall in London before Queen Elizabeth I of England, who recognises his status. He returns to Ireland on May 26 and resumes his rebellious activities by November.
January 17 – Huguenots are recognized under the Edict of Saint-Germain.
Council of Trent reconvened after a gap of 10 years.
First performance of Thomas Norton and Thomas Sackville's play Gorboduc before Queen Elizabeth I of England. It is the first known English tragedy and the first English language play to employ blank verse.
March 1 – Over 80(?) Huguenots are massacred by the ultra-Catholic Francis, Duke of Guise in Wassy-sur-Blaise, marking the start of the First War of Religion in France. Protestant forces led by Louis I de Bourbon, Prince de Condé and Gaspard de Coligny quickly seize control of Orléans, Rouen, and other cities throughout France.
March – English merchant Anthony Jenkinson has an audience with Ivan the Terrible in Moscow before continuing his second expedition through the Grand Duchy of Moscow to Qazvin, capital of the Safavid dynasty in Persia.
May 1 – Jean Ribault, French navigator, lands in Florida and later establishes a Huguenot colony at Charlesfort on Parris Island, off the coast of South Carolina.
July 12 – Fray Diego de Landa, acting Bishop of Yucatan, burns the sacred books of the Maya.
August – The beginning of the Wiesensteig witch trial.
September 20 – Treaty of Hampton Court between Queen Elizabeth I of England and Huguenot leader Louis, Prince of Condé.
September 22 – Maximilian, son of the Emperor Ferdinand I, succeeds as King of Bohemia.
October – John Hawkins initiates the English trans-Atlantic slave trade, shipping slaves from Sierra Leone on the Guinea Coast to Hispaniola in the Caribbean. As a result, the Spanish prohibit English ships from trading at their new world ports.
October 4 – English forces under Ambrose Dudley, 3rd Earl of Warwick, land at Le Havre to aid the Huguenots.
October 19 – La Herradura naval disaster, 25 ships sank in a storm and some 5000 people were killed.
October 26 – Rouen is captured by Royalist forces under Antoine de Bourbon, King of Navarre, who is mortally wounded.
November 5 – In Scotland, the rebellion of George Gordon, Earl of Huntly is crushed by James Stewart, Earl of Moray, at the Battle of Corrichie.
November 20 – Maximilian of Bohemia is elected King of the Romans.
December 19 – Battle of Dreux: Huguenot forces under Condé and Coligny, and Catholic forces under the ageing Anne, duc de Montmorency, and Francis, Duke of Guise, fight a bloody battle, narrowly won by the Catholic side. The official leaders of both armies (Condé and Montmorency) are captured in the battle.
The Mughal Emperor Akbar conquers Malwa and its last Sultan, Baz Bahadur, flees.
The Church of England approves the Thirty-Nine Articles of Religion, defining its doctrinal stance.
Dudley Grammar School is established and Gresham's School is granted a royal charter in England.
Fausto Sozzini publishes Brevis explicatio in primum Johannis caput, originating Socinianism.
Giacomo Barozzi da Vignola publishes Regola delli cinque ordini d'architettura (Rules of the Five Orders of Architecture); it will become in succeeding centuries the most published book in architectural history.
January – Edward Blount, English publisher (d. 1632)
January 12 – Charles Emmanuel I, Duke of Savoy (d. 1630)
January 13 – Mark Alexander Boyd, Scottish poet and soldier of fortune (d. 1601)
January 20 – Maria of Hanau-Münzenberg, German noblewoman (d. 1605)
January 20 – Ottavio Rinuccini, Italian composer (d. 1621)
February 15 – Rascas de Bagarris, French scholar (d. 1620)
February 15 – Maeda Toshinaga, Daimyo (d. 1614)
March 27 – Jacob Gretser, German Jesuit writer (d. 1625)
April or May – Jan Pieterszoon Sweelinck, Dutch composer (d. 1621)
April 21 – Valerius Herberger, German theologian (d. 1627)
April 24 – Xu Guangqi, Ming Dynasty Chinese politician, scholar and lay Catholic leader (d. 1633)
April 25 – Friedrich Wilhelm I, Duke of Saxe-Weimar, German noble (d. 1602)
May 6 – Pietro Bernini, Italian sculptor (d. 1629)
May 26 – James III, Margrave of Baden-Hachberg (d. 1590)
May 28 – John William, Duke of Jülich-Cleves-Berg (d. 1609)
June 24 – François de Joyeuse, Duke of Joyeuse (d. 1615)
June 26 – Anne of Ostfriesland, German noblewoman (d. 1621)
July 25 – Katō Kiyomasa, Japanese samurai (d. 1611)
August 17 – (baptised) – Hans Leo Hassler, German composer (d. 1612)
August 19 – Charles II de Bourbon-Vendôme, Roman Catholic cardinal (d. 1594)
September 1 – George, Count of Nassau-Dillenburg (1607-1620), then Count of Nassau-Dillenburg (1620-1623) (d. 1623)
September 21 – Vincenzo Gonzaga, Duke of Mantua and Montferrat (1587-1612) (d. 1612)
September 24 – Ercole, Lord of Monaco, Monegasque noble (d. 1604)
October 4 – Christian Sørensen Longomontanus, Danish astronomer (d. 1647)
October 19 – George Abbot, Archbishop of Canterbury (d. 1633)
November 25 – Lope de Vega, Spanish poet and dramatist (d. 1635)
December 10 – Roger de Saint-Lary de Termes, French noble (d. 1646)
December 14 – Sir Lionel Tollemache, 1st Baronet, English Baronet (d. 1621)
December 18 – Philipp Dulichius, German composer (d. 1631)
Isabella Andreini, Italian actress (d. 1604)
John Bull, English composer (d. 1628)
Henry Constable, English poet (d. 1613)
Samuel Daniel, English poet and historian (d. 1619)
Francis Godwin, English writer and prelate (d. 1633)
George Gordon, 1st Marquess of Huntly (d. 1636)
Juan de Jáuregui, attempted assassin of William I of Orange (d. 1582)
Natsuka Masaie, Japanese daimyo (d. 1600)
Richard Neile, English churchman (d. 1640)
Henry Spelman, English antiquary (d. 1641)
Maeda Toshinaga, Japanese nobleman (d. 1614)
Cornelis van Haarlem, Dutch painter (d. 1638)
Xu Guangqi, Chinese agronomist, astronomer, and mathematician (d. 1633)
January – Ilie II Rareş, Prince of Moldavia (b. 1531)
January 9 – Amago Haruhisa, Japanese samurai and warlord (b. 1514)
January 25 – Charles Wriothesley, officer of arms (b. 1508)
May 14 – Lelio Sozzini, Italian Protestant theologian (b. 1525)
July 23 – Götz von Berlichingen, German knight and mercenary (b. 1480)
September 5 – Katharina Zell, German Protestant reformer (b. 1497)
October 9 – Gabriele Falloppio, Italian anatomist (b. 1523)
October 13 – Claudin de Sermisy, French composer (b. 1495)
October – George Gordon, 4th Earl of Huntly (b. 1514)
November 7 – Maldeo Rathore, Rao of Marwar (b. 1511)
November 12 – Pietro Martire Vermigli, Italian theologian (b. 1500)
November 17 – Antoine de Bourbon, father of Henry IV of France (b. 1518)
December 6 – Jan van Scorel, Dutch painter (b. 1495)
December 7 – Adrian Willaert, Flemish composer (b. c. 1490)
December 17 – Eleonora di Toledo, Grand Duchess of Tuscany (b. 1522)
Cristóbal de Guzmán Cecetzin, Tlatoani of Tenochtitlan and Governor of San Juan Tenochtitlan
Matteo Bandello, Italian novelist (b. 1480)
Nicholas Grimald, English poet and theologian (b. 1519)
probable - Lutfi Pasha, poet and juridical scholar of slave origin
Year 1562 (MDLXII) was a common year starting on Thursday (link will display the full calendar) of the Julian calendar.