|Covid-19|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 take place in Kalmar in 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 24 – The 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 this 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 Șelimbăr, leading to the first recorded unification of the Romanians.
November 10 – Åbo Bloodbath takes place in Åbo in Swedish Finland.
November – Persian embassy to Europe (1599–1602): A Persian embassy arrives in Moscow.
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, Burma).
The first Capuchin friar is entombed in the Capuchin catacombs of Palermo.
A Dutch fleet returns to Amsterdam, carrying 600,000 pounds of pepper and 250,000 pounds of cloves and nutmeg.
The Italian city of Pompeii is rediscovered more than 1500 years after its burial following the eruption of Mount Vesuvius in 79.
January 1 – Jirgalang, Qing dynasty prince (d. 1655)
January 22 – Robert Petre, 3rd Baron Petre, English Baron (d. 1638)
January 31 – Juraj V Zrinski, Ban of Croaita (d. 1626)
Duke Friedrich of Saxe-Altenburg, Third son of Duke Friedrich Wilhelm I of Saxe-Weimar (d. 1625)
Thomas Whitmore, English lawyer and politician who sat in the House of Commons (d. 1677)
February 13 – Pope Alexander VII (d. 1667)
March 1 – John Mennes, Royal Navy admiral (d. 1671)
March 3 – Juan Alfonso Enríquez de Cabrera, Viceroy of Sicily and Viceroy of Naples (d. 1647)
March 13 – John Berchmans, Belgian Jesuit scholastic and saint (d. 1621)
March 22 – Anthony van Dyck, Flemish painter (d. 1641)
March 23 – Thomas Selle, German baroque composer (d. 1663)
March 28 – Witte Corneliszoon de With, famous Dutch naval officer of the 17th century (d. 1658)
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 (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 12 – Sir William Curtius FRS, German magistrate, English baronet; official resident of the English Crown in the Holy Roman Empire, (d. 1678).
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 (d. 1670)
September 20 – Christian, Duke of Brunswick-Lüneburg-Wolfenbüttel, German Protestant military leader (d. 1626)
September 25 – Francesco Borromini, Swiss sculptor and architect (d. 1667)
September 30 – Frances Seymour, Duchess of Somerset (d. 1674)
Samuel Clarke, English writer and priest (d. 1683)
Étienne Moulinié, French Baroque composer (d. 1676)
October 11 – Abraham de Fabert, Marshal of France (d. 1662)
October 15 – Cornelis de Graeff, Dutch mayor (d. 1664)
October 27 – Niels Trolle, Governor General of Norway (d. 1667)
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, Prince-bishop (d. 1658)
Maria Eleonora of Brandenburg, German princess and queen consort of Sweden (d. 1655)
Ottavio Piccolomini, Austrian-Italian field marshal (d. 1656)
November 13 – Otto Christoph von Sparr, German general (d. 1668)
November 15 – Werner Rolfinck, Physician, chemist, botanist, philosopher (d. 1673)
November 29 – Peter Heylin, English ecclesiastic and author of many polemical (d. 1662)
November 30 – Andrea Sacchi, Italian painter of High Baroque Classicism (d. 1661)
Thomas Bruce, 1st Earl of Elgin, Scottish nobleman (d. 1663)
Alexander Daniell, Sole proprietor of the Manor of Alverton, Cornwall (d. 1668)
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 29 – Gabriel Bucelin, German historian (d. 1681)
John Alden, English settler of Plymouth Colony (d. 1687)
Robert Blake, English admiral (d. 1657)
Stefan Czarniecki, Polish military commander (d. 1665)
Lucy Hay, Countess of Carlisle, English socialite (d. 1660)
Charlotte Stanley, Countess of Derby defender of Latham House (d. 1664)
January 13 – Edmund Spenser, English poet (b. 1552)
January 22 – Cristofano Malvezzi, Italian composer (b. 1547)
February 8 – Robert Rollock, first principal of the university of Edinburgh (b. 1555)
April 10 – Gabrielle d'Estrées, mistress of King Henry IV of France (b. 1571)
April 14 – Henry Wallop, English statesman (b. c. 1540)
April 27 – Maeda Toshiie, Japanese samurai and warlord (b. 1538)
June 14 – Kōriki Masanaga, Japanese military commander (b. 1558)
July 11 – Chosokabe Motochika, Sengoku Period Daiymo
Beatrice Cenci, Italian noblewoman who conspired to kill her father (b. 1577)
Luca Marenzio, Italian composer (b. 1553)
September 1 – Cornelis de Houtman, Dutch explorer (b.1565)
November 7 – Gasparo Tagliacozzi, Italian surgeon (b. 1546)
November 8 – Francisco Guerrero, Spanish composer (b. 1528)
December 14 – Joan Boyle, first wife of Richard Boyle, 1st Earl of Cork (b. 1568)
After December 18 – Minye Kyawswa II of Ava, Burmese defecting crown prince of the Toungoo Empire (killed by invading forces) (b. 1567)
Kwon Yul, Korean military commander (b. 1537)
Chand Bibi, Indian woman warrior (by her own troops) (b. 1550)
1599 (MDXCIX) was a common year starting on Friday (dominical letter C) of the Gregorian calendar and a common year starting on Monday (dominical letter G) of the Julian calendar, the 1599th year of the Common Era (CE) and Anno Domini (AD) designations, the 599th year of the 2nd millennium, the 99th year of the 16th century, and the 10th and last year of the 1590s decade. As of the start of 1599, the Gregorian calendar was 10 days ahead of the Julian calendar, which remained in localized use until 1923.