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1599 (MDXCIX) was a common year starting on Friday of the Gregorian calendar and a common year starting on Monday of the Julian calendar. As of the start of 1599, the Gregorian calendar was 10 days ahead of the Julian calendar.
- January 8 - The Jesuit educational plan, known as the Ratio Studiorum, is issued.
- March 12 - Robert Devereux, 2nd Earl of Essex, is appointed Lord Lieutenant of Ireland, by Queen Elizabeth I of England.
- April 23 - The Earl of Essex arrives in Dublin at the head of 16,000 troops, the largest army ever seen in Ireland.
- May 16 - The Kalmar Bloodbath takes place in Kalmar, Sweden.
- May 29 - Essex takes Cahir Castle, supposedly the strongest in Ireland, after a short siege.
- June 20 - The Synod of Diamper is convened.
- July - Second Dutch Expedition to Indonesia: A Dutch fleet returns to Amsterdam, carrying 600,000 pounds of pepper and 250,000 pounds of cloves and nutmeg.
- July 24 - Swedish King Sigismund III Vasa is dethroned by his uncle Duke Charles, who takes over as regent of the realm until 1604, when he becomes King Charles IX.
- August 15 - First Battle of Curlew Pass: Irish forces defeat the English.
- September 21 - The first reported performance at the Globe Theatre in London (erected over Spring/Summer), a presentation of Shakespeare's Julius Caesar (probably new to that year), is recorded by Swiss traveller Thomas Platter the Younger.
- September 28 - The Earl of Essex arrives back in England, disobeying the Queen's strict orders.
- October 18 - Battle of Sellenberk: Michael the Brave, Prince of Wallachia, defeats the army of Andrew Báthory near ?elimb?r, leading to the first recorded unification of the Romanians.
- November 10 - The Åbo Bloodbath takes place in Åbo, Swedish Finland.
- November - Persian embassy to Europe (1599-1602): A Persian embassy arrives in Moscow.
- December 19 - The forces of Minye Thihathu II of Toungoo and his ally Min Razagyi of the Kingdom of Mrauk U end the First Toungoo Empire by capturing Pegu (modern-day Bago, Myanmar).
- April 9 - Sir Thomas Mauleverer, 1st Baronet (d. 1655)
- April 17 - Patrick Fleming, Irish Franciscan friar and scholar (murdered) (d. 1631)
- April 25 - Oliver Cromwell, Lord Protector of England, Scotland, and Ireland (d. 1658)
- May 16 - Nicolaes Olycan, Dutch businessman (d. 1639)
- May 30 - Samuel Bochart, French Protestant biblical scholar (d. 1667)
- June 1 - Elizabeth Lucretia, Duchess of Cieszyn, Duchess suo jure of Cieszyn (d. 1653)
- June 6 - Diego Velázquez, Spanish painter (d. 1660)
- July 23 - Stephanius, Danish historian (d. 1650)
- July 27 - Albert IV, Duke of Saxe-Eisenach (1640-1644) (d. 1644)
- August 11 - Christian II, Prince of Anhalt-Bernburg (1630-1656) (d. 1656)
- August 13 - Johannes Buxtorf II, Swiss theologian (d. 1664)
- August 14 - Méric Casaubon, English classicist (d. 1671)
- August 16 - Diego López Pacheco, 7th Duke of Escalona, Spanish noble (d. 1653)
- August 22 - Agatha Marie of Hanau, German noblewoman (d. 1636)
- September 7 - Jacob Westerbaen, Dutch poet (d. 1670)
- September 20 - Christian, Duke of Brunswick-Lüneburg-Wolfenbüttel, German Protestant military leader (d. 1626)
- September 24 - Adam Olearius, German scholar (d. 1671)
- September 25 - Francesco Borromini, Swiss sculptor and architect (d. 1667)
- September 30 - Frances Seymour, Duchess of Somerset (d. 1674)
- October 10
- October 11 - Abraham de Fabert, Marshal of France (d. 1662)
- October 15 - Cornelis de Graeff, Dutch mayor (d. 1664)
- October 28 - Marie of the Incarnation, French foundress of the Ursuline Monastery in Quebec (d. 1672)
- October 31 - Denzil Holles, 1st Baron Holles, English statesman and writer (d. 1680)
- November 5 - Carlo Emanuele Madruzzo, Italian prince-bishop (d. 1658)
- November 11
- November 13 - Otto Christoph von Sparr, German general (d. 1668)
- November 15 - Werner Rolfinck, German physician, chemist, botanist and philosopher (d. 1673)
- November 29 - Peter Heylin, English ecclesiastic and author of many polemical works (d. 1662)
- November 30 - Andrea Sacchi, Italian painter of High Baroque Classicism (d. 1661)
- December 2
- December 11 - Pieter Codde, Dutch painter (d. 1678)
- December 14 - Charles Berkeley, 2nd Viscount Fitzhardinge, English politician (d. 1668)
- December 16 - Jacques Vallée, Sieur Des Barreaux, French poet (d. 1673)
- December 20 - Niels Trolle, Governor General of Norway (d. 1667)
- December 29 - Gabriel Bucelin, German historian (d. 1681)
- January 13 - Edmund Spenser, English poet (b. 1552)
- January 22 - Cristofano Malvezzi, Italian composer (b. 1547)
- February 8 - Robert Rollock, Scottish Presbyterian, first principal of the university of Edinburgh (b. 1555)
- March 19 - Stanis?aw Radziwi, Grand Marshal of Lithuania (b. 1559)
- April 10 - Gabrielle d'Estrées, mistress of King Henry IV of France (b. 1573)
- April 14 - Henry Wallop, English statesman (b. c. 1540)
- April 22 - Lorenz Scholz von Rosenau, German botanist (b. 1552)
- April 27 - Maeda Toshiie, Japanese samurai and warlord (b. 1538)
- May 12 - Sultan Murad Mirza, Mughal prince (b. 1570)
- May 28 - Maria of Nassau, Dutch Countess (b. 1539)
- June 2 - Philipp V, Count of Hanau-Lichtenberg (b. 1541)
- June 14 - K?riki Masanaga, Japanese military commander (b. 1558)
- June 29 - Archduchess Catherine Renata of Austria, Austrian archduchess (b. 1576)
- July - Kwon Yul, Korean military commander (b. 1537)
- July 11 - Ch?sokabe Motochika, Japanese Sengoku Period daimy?
- August 22 - Luca Marenzio, Italian composer (b. 1553)
- September 1 - Cornelis de Houtman, Dutch explorer (b.1565)
- September 11 - Beatrice Cenci, Italian noblewoman (executed for patricide) (b. 1577)
- August 8 - Song Ik-pil, Korean scholar (b. 1534)
- October 18 - Daniel Adam z Veleslavína, Czech lexicographer (b. 1546)
- November 3 - Andrew Báthory, deposed Prince of Transylvania (decapitated) (b. c. 1563)
- November 7 - Gasparo Tagliacozzi, Italian surgeon (b. 1545)
- November 8 - Francisco Guerrero, Spanish composer (b. 1528)
- November 22 - Nanbu Nobunao, Japanese daimy? (b. 1546)
- December 13 - Enrico Caetani, Italian Catholic cardinal (b. 1550)
- December 14 - Joan Boyle, English noble, first spouse of Richard Boyle, 1st Earl of Cork (b. 1578)
- December 27 - Francisco Pérez de Valenzuela, Spanish noble (b. 1528)
- After December 18 - Minye Kyawswa II of Ava, Burmese defecting crown prince of the Toungoo Empire (killed by invading forces) (b. 1567)
- date unknown - Chand Bibi, Indian regent and warrior (b. 1550)