The 1560s decade ran from January 1, 1560, to December 31, 1569.
- February 27 – Treaty of Berwick: Terms are agreed upon, with the Lords of the Congregation in the Kingdom of Scotland, for forces of the Kingdom of England to enter Scotland, to expel French troops defending the Regency of Mary of Guise.
- March 7 – A Spanish-led expedition, commanded by Juan de la Cerda, 4th Duke of Medinaceli, overruns the Tunisian island of Djerba.
- March 17 – Leaders of the Amboise conspiracy, including Godefroy de Barry, seigneur de La Renaudie, make an unsuccessful attempt to storm the château of Amboise, where the young French king and queen are residing. La Renaudie is subsequently caught and executed, along with over 1,000 of his followers.
- April 15 – Denmark buys the Estonian island of Saaremaa, from its last prince-bishop.
- May 11 – Battle of Djerba: The Ottoman fleet, commanded by Piali Pasha, overwhelms a large joint European (mainly Spanish) fleet, sinking about half its ships.
- June 12 – Battle of Okehazama: Oda Nobunaga defeats Imagawa Yoshimoto.
- July 6 – The Treaty of Edinburgh is signed between England, France and Scotland, ending the Siege of Leith. The French withdraw from Scotland, largely ending the Auld Alliance between the two countries, and also ending the wars between England and its northern neighbour.
- August 2 – Livonian War – Battle of Ergeme: Russians defeat the Livonian Brothers of the Sword, precipitating the dissolution of the order.
- August 17 – The Scottish Reformation Parliament adopts a Protestant confession of faith and rejects papal authority, beginning the Scottish Reformation, and disestablishing Roman Catholicism in Scotland.
- August 21 – A total eclipse of the sun is observable in Europe.
- September 29 – Eric XIV becomes King of Sweden, upon the death of his father Gustav Vasa.
- December 5 – King Francis II of France dies aged 16 of an ear infection at Orléans, widowing the 17-year-old Mary, Queen of Scots. He is succeeded by his younger brother Charles IX at the age of 10 with his mother (Mary's mother-in-law), Catherine de' Medici, as regent of France.
- The complete Geneva Bible is published.
- The first tulip bulb is brought from Constantinople to the Netherlands (probable date).
- The first scientific society, the Academia Secretorum Naturae, is founded in Naples by Giambattista della Porta.
- Solihull School is founded in the West Midlands of England.
- The oldest surviving violin (dated inside), known as the Charles IX, is made in Cremona, in northern Italy.
- Bairam Khan loses power in the Mughal Empire.
- The Mongols invade and occupy Qinghai.
- The great age of piracy in the Caribbean starts around this time.
- January 31 – The Edict of Orleans suspends the persecution of the Huguenots in France.
- March 1 – Kingston Grammar School is founded in England.
- April 14 – The citizens of Nuremberg see what appears to be an aerial battle, followed by the appearance of a large black triangular object and a large crash (with smoke) outside the city. A news notice (an early form of newspaper) is printed on April 14, describing the event.
- May 8 – Madrid is declared the capital of Spain, by Philip II.
- June 4 – Old St Paul's Cathedral in the City of London is badly damaged by fire, and the spire is destroyed after being struck by lightning. The spire is not rebuilt.
- June 4 – The nobility of Harrien-Wierland and the town of Reval (on June 6) of the Livonian Order swear allegiance to Sweden.
- June 25 – Francis Coxe, an English astrologer, is pilloried at Cheapside in London, and makes a public confession of his involvement in "sinistral and divelysh artes".
- June 29 – Erik XIV is crowned King of Sweden.
- July – Arauco War: The hated encomendero Pedro de Avendaño and two other Spaniards are killed, triggering the Second Great Rebellion of the Mapuche.
- July 12 – Saint Basil's Cathedral in Moscow (started in 1534) is finished.
- August – English merchant Anthony Jenkinson arrives in Moscow on his second expedition to the Grand Duchy of Moscow.
- August 19 – Mary, Queen of Scots, is denied passage through England after returning from France. She arrives at Leith, Scotland on August 19.
- September – Protestant reformer John Knox has a three-day debate in Maybole, Ayrshire, Scotland with Quintin Kennedy, commendator of Crossraguel Abbey, on transubstantiation. The result is inconclusive, but Kennedy is fighting a losing battle against the Reformation, which had been confirmed by the Scottish government in 1560.
- October 18 – Fourth Battle of Kawanakajima: Takeda Shingen defeats Uesugi Kenshin, in the climax of their ongoing conflicts.
- November 28 – Treaty of Vilnius was concluded during the Livonian War, between the Livonian Confederation and the Polish–Lithuanian Commonwealth. With the treaty, the non-Danish and non-Swedish part of Livonia, with the exception of the Free imperial city of Riga, subjected itself to Polish king and Grand Duke of Lithuania, Sigismund II Augustus with the Pacta subiectionis (Provisio ducalis). In turn, Sigismund granted protection from the Tsardom of Russia and confirmed the Livonian estates' traditional privileges, laid out in the Privilegium Sigismundi Augusti.
- The first Calvinists settle in England, after fleeing Flanders.
- The Anglo-Genevan metrical psalter is published, including the Old 100th, the version of the hymn All People That on Earth Do Dwell made from Psalm 100, attributed to the probably-Scottish clergyman and biblical translator William Kethe, exiled in Geneva.
- Ruy López de Segura develops modern techniques of chess playing in Spain.
- William Baldwin's Beware the Cat (written early 1553), an early example of extended fiction (specifically horror fiction) in English, is published anonymously in London. This edition appears to have been suppressed, and no copies survive.
- Between 1561 and 1670, 3,229 alleged witches are executed in southwestern Germany, most by burning.
- January 6 – Shane O'Neill of Tír Eoghain 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.
- January 18
- 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, South Carolina
- July 12 – Fray Diego de Landa, acting Bishop of Yucatan, burns the sacred books of the Maya.
- August – The Wiesensteig witch trial begins.
- September 20 – The Treaty of Hampton Court, between Queen Elizabeth I of England and Huguenot leader Louis, Prince of Condé, is signed.
- September 22 – Maximilian, son of the Emperor Ferdinand I, succeeds as king of the Kingdom 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: Twenty-five ships sink in a storm, and some 5,000 people are killed.
- October 26 – Rouen is captured by Royalist forces under Antoine de Bourbon, King of Navarre, who is mortally wounded.
- November 5 – Battle of Corrichie in Scotland: The rebellion of George Gordon, Earl of Huntly is crushed by James Stewart, Earl of Moray.
- November 20 – Maximilian of Bohemia is elected King of the Romans.
- December 19 – Battle of Dreux: Huguenot and Catholic forces fight a bloody battle, narrowly won by the Catholic side. The official leaders of both armies are captured in the battle.
- 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.
- February 1 – Sarsa Dengel succeeds his father Menas, as Emperor of Ethiopia.
- February 18 – Francis, Duke of Guise, is assassinated while besieging Orléans.
- March 19 – The Edict of Amboise is signed at the Château d'Amboise by Catherine de' Medici, acting as regent for her son Charles IX of France, having been negotiated between the Huguenot Louis, Prince of Condé, and Anne, duc de Montmorency, Constable of France. It accords some toleration to the Huguenots, especially to aristocrats. It officially ends the first phase of the French Wars of Religion, and the combined Huguenot and royal armies then march north to besiege the English in Le Havre.
- May 25 – Elizabeth College, Guernsey founded, by order of Queen Elizabeth I
- May 30 – At Bornholm, the Danish fleet fires on the Swedish navy, leading to a Danish defeat and precipitating the Northern Seven Years' War.
- July 28 – The English surrender Le Havre to the French after a siege.
- August 13 – Northern Seven Years' War: War against the Kingdom of Sweden is declared by Denmark–Norway and the Free City of Lübeck.
- August 18 – Merchants from the Bungo Province destroy the Portuguese settlement in Yokoseura, Japan
- September 4 – Northern Seven Years' War: King Frederick II of Denmark, advancing from Halland, takes Älvsborg fortress from Sweden.
- December 4 – The Council of Trent (opened December 13, 1545) officially closes. It reaffirms all major Roman Catholic doctrines, and declares the Deuterocanonical books of the Old Testament to be canonical, along with the rest of the Bible. Chapter 1, Session 24, promulgates the decree Tametsi, stipulating that for a marriage to be valid, consent (the essence of marriage) as expressed in the vows has to be given publicly before witnesses, one of whom has to be the parish priest.
- January 26 – Livonian War – Battle of Ula: A Lithuanian surprise attack results in a decisive defeat of the numerically superior Russian forces.
- March 25 – Battle of Angol in Chile: Spanish Conquistador Lorenzo Bernal del Mercado defeats and kills the toqui Illangulién.
- June 22 – French settlers abandon Charlesfort, the first French attempt at colonizing what is now the United States, and establish Fort Caroline in Florida.
- July – English merchant Anthony Jenkinson returns to London from his second expedition to the Grand Duchy of Moscow, having gained a considerable extension of trading rights for the English Muscovy Company.
- September 4 – The Ronneby Bloodbath take place in Ronneby, Denmark (now in Sweden).
- September 10 – Battle of Kawanakajima in Japan: Takeda Shingen fights the forces of Uesugi Kenshin for the final time, to a draw.
- November 21 – Spanish Conquistador Miguel López de Legazpi sails from Mexico. Later, he will conquer the Philippine Islands, founding Manila.
- First recorded report of a 'rat king'.
- approx. date – Idris Alooma starts to rule the Kanem-Bornu Empire.
- January – In Russia, it is the beginning of the Oprichnina, under Ivan the Terrible.
- January 23 – Battle of Talikota: The Vijayanagara Empire, the last Hindu kingdom in South India, is greatly weakened by the Deccan sultanates.
- February 13 – Spanish Conquistador Miguel López de Legazpi lands with his troops on the shores of Cebu Island, in the Philippines.
- March 1 – The city of Rio de Janeiro, Brazil, is founded as São Sebastião do Rio de Janeiro by Estácio de Sá.
- March 16 – Spanish Conquistador Miguel Lopez de Legazpi makes a Sandugan with the Datu Sikatuna, in the island of Bohol Philippines.
- April 27 – Cebu City is established as San Miguel by López de Legazpi, becoming the first Spanish settlement in the Philippines.
- May 18 – Ottoman troops land on the island of Malta, beginning the Siege of Malta.
- June 4 – The Treaty of Cebu is signed between Miguel Lopez de Legazpi, representing Philip II of Spain and Rajah Tupas of Cebu. This treaty effectively created Spanish suzerainty over Cebu.
- June 17 – Matsunaga Hisahide assassinates the 13th Ashikaga shōgun, Ashikaga Yoshiteru.
- July 29 – Mary, Queen of Scots, widowed, marries Henry Stuart, Lord Darnley.
- August 6 – Sark is granted as a Fief, by Elizabeth I, to Hellier de Carteret, Seigneur of Saint Ouen.
- August 28 – St. Augustine, Florida (named after St. Augustine), is established. It is the oldest remaining European settlement in the United States.
- September 4 – The Spanish fleet of Pedro Menéndez de Avilés lands on modern-day Florida, to oust the French under Jean Ribault. He later destroys the French colony of Fort Caroline.
- September 8 – Pedro Menéndez de Avilés settles in St. Augustine, Florida.
- September 11 – The Knights of Malta lift the Siege of Malta, after four months.
- October – The first Martello tower, the Tour de Mortella, designed by Giovan Giacomo Paleari Fratino (el Fratin), is completed as part of the Genovese defence system at Mortella (Myrtle) Point, in Upper Corsica.
- October 18 – Battle of Fukuda Bay: Ships belonging to the Matsura clan of Japan fail to capture the Portuguese trading carrack, in the first recorded naval battle between Japan and the West.
- The pencil is first documented by Conrad Gesner; it is becoming common in England.
- John Beddoes School is founded at Presteigne, Wales.
- Herlufsholm School is founded in Denmark.
- Huntingdon Grammar School is established in England.
- January 7 – Pope Pius V succeeds Pope Pius IV, as the 225th pope.
- February 24 – In one of the first gun assassination's in Japanese history if not world history, Mimura Iechika is shot dead by two brothers Endo Matajiro and Yoshijiro sent by his rival Ukita Naoie.
- March 28 – The foundation stone of Valletta, which will become Malta's capital city, is laid by Jean Parisot de Valette, Grand Master of the Sovereign Military Order of Malta.
- April 5 – The Compromise of Nobles is presented to Margaret of Parma, Governor of the Habsburg Netherlands, but it succeeds only in delaying the beginning of the Eighty Years' War in the Netherlands.
- August 6 – The Siege of Szigetvár has begun by Suleiman the Magnificent, Sultan of the Ottoman Empire.
- August 10 – Beeldenstorm: Calvinists engage in widespread destruction of religious art in the Low Countries. On August 25, the vandalism reaches Leiden.
- September 7 – Suleiman the Magnificent dies in his tent at the Siege of Szigetvár, and Selim II succeeds him as Sultan of the Ottoman Empire.
- September 8 – The Siege of Szigetvár ends in battle, with 2,300 Hungarian and Croatian defenders, including their general, Nikola Šubić Zrinski, annihilated by an army of 90,000 soldiers of the Ottoman Empire, under Sokollu Mehmed Pasha.
- The Spanish gold escudo, worth 16 silver reales, is first minted during the reign of Philip II of Spain.
- Pope Pius V expels most prostitutes from Rome, and the Papal States.
- Between July 19, 1566 and July 7, 1567 – The first bridge crossing the Neretva River at Mostar (in modern-day Bosnia and Herzegovina) is completed by the Ottoman Empire. The white marble bridge becomes known as Stari Most ("Old Bridge").
- January – A Spanish force under the command of Captain Juan Pardo establishes Fort San Juan, in the Native American settlement of Joara. The fort is the first European settlement in present-day North Carolina.
- January 20 – Battle of Rio de Janeiro: Portuguese forces under the command of Estácio de Sá definitively drive the French out of Rio de Janeiro.
- January 23 – After 45 years' reign, the Jiajing Emperor dies in the Forbidden City of China.
- February 4 – The Longqing Emperor ascends the throne of the Ming dynasty.
- February 10 – Henry Stuart, Lord Darnley, husband of Mary, Queen of Scots, is murdered at the Provost's House in Kirk o' Field, Edinburgh.
- March 13 – A Spanish mercenary army surprises and kills a band of rebels in the Battle of Oosterweel near Antwerp in the Habsburg Netherlands, beginning the Eighty Years' War.
- May 15 – Mary, Queen of Scots, marries James Hepburn, 4th Earl of Bothwell.
- May 24 – The infamous Sture Murders take place at Uppsala Castle in Sweden.
- June 15 – Battle of Carberry Hill: Mary, Queen of Scots, is defeated by the Scottish nobles and imprisoned in Loch Leven Castle.
- July 24 – Mary, Queen of Scots, is forced to abdicate and replaced by her one-year-old son James VI.
- July 25 – The city of Santiago de León de Caracas', Venezuela is founded by Diego de Losada.
- July 29 – James VI is crowned at Stirling.
- August 22 – The Duke of Alba is sent to the Netherlands with a strong Spanish force, to suppress unrest there. He replaces Margaret of Parma as Governor of the Netherlands. Prince William of Orange is outlawed, and Lamoral, Count of Egmont imprisoned.
- September 9 – At a dinner, the Duke of Alba arrests Lamoral, Count of Egmont and Philip de Montmorency, Count of Horn for treason.
- September 29 – The Second War of Religion begins in France, when Louis, Prince of Condé and Gaspard de Coligny fail in an attempt to capture King Charles IX and his mother at Meaux. The Huguenots do capture several cities (including Orléans), and march on Paris.
- October 7 – Bible translations into Welsh: The New Testament is first published in Welsh, in William Salesbury's translation from the Greek.
- November 10 – Battle of Saint-Denis: Anne de Montmorency, with 16,000 Royalists, falls on Condé's 3,500 Huguenots. The Huguenots surprisingly hold on for some hours before being driven off. Montmorency is mortally wounded.
- King Frederick II of Denmark and Norway founds Fredrikstad in Norway.
- Construction of Villa Capra "La Rotonda" in Vicenza, designed by Andrea Palladio, begins. It will be one of the most influential designs in the history of architecture.
- Rugby School, one of the oldest public schools in England, is founded.
- Although sparse maritime trade existed since its founding, the Ming dynasty government of China officially revokes the haijin maritime trade ban, reinstating foreign trade with all countries except Japan.
- January 6–13 – In the Eastern Hungarian Kingdom, the delegates of Unio Trium Nationum to the Diet of Torda make Europe's first declaration of religious freedom, adopted on January 28 as the Edict of Torda.
- February 17 – Treaty of Adrianople (sometimes called the Peace of Adrianople): The Habsburgs agree to pay tribute to the Ottomans.
- March 23 – The Peace of Longjumeau ends the Second War of Religion in France. Again Catherine de' Medici and Charles IX make substantial concessions to the Huguenots.
- May 2 – Mary, Queen of Scots, escapes from Loch Leven Castle.
- May 13 – Battle of Langside: The forces of Mary, Queen of Scots are defeated by a confederacy of Scottish Protestants, under James Stewart, Earl of Moray, her half-brother.
- May 16 – Mary, Queen of Scots, flees to England.
- May 19 – Queen Elizabeth I of England arrests Mary, Queen of Scots.
- May 23 – Battle of Heiligerlee: Troops under Louis of Nassau, brother of William I of Orange, defeat a smaller loyalist force under the Duke of Arenberg, in an attempt to invade the Northern Netherlands. This effectively begins the Eighty Years' War.
- July 21 – Battle of Jemmingen: The main Spanish army of the Duke of Alva utterly defeats Louis of Nassau's invading army, in the Northeastern Netherlands.
- August 18 – The Third War of Religion begins in France, after an unsuccessful attempt by the Royalists to capture Condé and Coligny, the Huguenot leaders.
- September 23 – Battle of San Juan de Ulúa (Anglo-Spanish War): In the Gulf of Mexico, a Spanish fleet forces English privateers under John Hawkins to end their campaign.
- September 29 – The Swedish king Eric XIV is deposed, by his half-brothers John and Charles. John proclaims himself king John III the next day.
- October 5 – William I of Orange invades the southeastern Netherlands.
- October 20 – Battle of Jodoigne: Spanish forces under the Duke of Alva destroy Orange's rearguard. Orange abandons his offensive.
- The Russo-Turkish War begins in Astrakhan.
- Ashikaga Yoshiaki is installed as Shōgun, beginning the Azuchi–Momoyama period in Japan.
- Akbar the Great of the Mughal Empire besieges and captures the massive Chittor Fort, in northern India.
- Polybius' The Histories are first translated into English, by Christopher Watson.
- Huguenots besiege Chartres.
- A Spanish expedition under Álvaro de Mendaña de Neira discovers the Solomon Islands.
- January 11–May 6 – The first recorded lottery in England is performed nonstop, at the west door of St Paul's Cathedral. Each share costs ten shillings, and proceeds are used to repair harbours, and for other public works.
- March 13 – Battle of Jarnac: Royalist troops under Marshal Gaspard de Tavannes surprise and defeat the Huguenots under the Prince of Condé, who is captured and murdered. A substantial proportion of the Huguenot army manages to escape, under Gaspard de Coligny.
- June 10 – German Protestant troops reinforce Coligny, near Limoges.
- July 1 – The Union of Lublin unites the Kingdom of Poland and the Grand Duchy of Lithuania into a single state, the Polish–Lithuanian Commonwealth, following votes in the Assemblies of three Lithuanian provinces (Volhynia, Ukraine and Podlasie) in favour of the incorporation.
- July–September – Huguenot forces under Coligny and 15-year-old Prince Henry of Navarre besiege Poitiers.
- August 24 – Battle of Orthez: Huguenot forces under Gabriel, comte de Montgomery defeat Royalist forces under General Terride, in French Navarre. Catholics surrender under the condition that their lives will be spared. Huguenots agree, but then massacre the Catholics anyway.
- September – A Royalist army under the Duc d'Anjou and Marshal Tavannes forces Coligny to abandon the siege of Poitiers.
- October 3 – Battle of Moncontour: The Royalist forces of Tavannaes and Anjou defeat Coligny's Huguenots.
- November–December – Rising of the North in England: Three northern earls lead a rebellion against Queen Elizabeth I, in an attempt to place the Catholic Mary, Queen of Scots, on the English throne, but are driven out of the country.
- The Mercator projection is first used in Gerardus Mercator's world map, Nova et Aucta Orbis Terrae Descriptio ad Usum Navigantium Emendata.
- Damcar appears on the Mercator map or Arabia.
- The trade compact of 1536 is renewed, exempting French merchants from Ottoman law, and allowing them to travel, buy and sell throughout the sultan's dominions, and to pay low customs duties on French imports and exports.
- Akbar founds Fatehpur Sikri, to honor the Muslim holy man Shaikh Salim Chisti, who has foretold the birth of Akbar's son and heir, Jahangir.
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