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Year 1499 (MCDXCIX) was a common year starting on Tuesday (link will display the full calendar) of the Julian calendar.

• January 8 – Louis XII of France marries Anne of Brittany, in accordance with a law set by his predecessor, Charles VIII.^[1]
• May 19 – 18-year-old Catherine of Aragon, the future first wife of Henry VIII of England, is married by proxy to his brother, 12-year-old Arthur, Prince of Wales.
• July 22 – Battle of Dornach: The Swiss decisively defeat the army of Maximilian I, Holy Roman Emperor.^[2]
• July 28 – First Battle of Lepanto: The Turkish navy wins a decisive victory over the Venetians.
• August – Polydore Vergil completes De inventoribus rerum, the first modern history of inventions.
• August 24 – Lake Maracaibo is discovered, by Alonso de Ojeda and Amerigo Vespucci.
• September 18 – Vasco da Gama arrives at Lisbon, returning from India, and is received by King Manuel of Portugal.^[3]
• September 22 – Treaty of Basel: Maximilian is forced to grant the Swiss de facto independence.
• October 25 – The Pont Notre-Dame in Paris, constructed under Charles VI of France, collapses into the Seine.^[4]
• November 5 – The Catholicon is published in Tréguier (Brittany). This Breton–greek–Latin dictionary had been written in 1464 by Jehan Lagadeuc. It is the first dictionary of either French or Breton.
• November 23 – Perkin Warbeck, pretender to the throne of England, is hanged for reportedly attempting to escape from the Tower of London.
• November 28 – Edward Plantagenet, 17th Earl of Warwick, last male member of the House of York, is executed for reportedly attempting to escape from the Tower of London.
• December 18 – The Rebellion of the Alpujarras (1499–1501) begins in the Kingdom of Granada (Crown of Castile) against the forced conversions of Muslims in Spain.

• The French under Louis XII seize Milan, driving out Duke Ludovico Sforza; Leonardo da Vinci flees to Venice.
• Montenegro, the last free monarchy in the Balkans, is annexed by the Ottoman Empire, as part of the sanjak of Shkodër, and Stefan II Crnojević is removed from office.
• Johannes Trithemius inadvertently reveals interests in magic by writing a letter to a Carmelite friar about a treatise he is writing on steganography.
• Heinrich Cornelius Agrippa matriculates at Cologne University.
• Giggleswick School is founded by Reverend James Carr in England.

• January 15 – Samuel Maciejowski, Polish bishop (d. 1550)
• January 20 – Sebastian Franck, German humanist (d. 1543)
• January 29 – Katharina von Bora, German nun, wife of Martin Luther (d. 1552)
• February 10 – Thomas Platter, Swiss humanist scholar and writer (d. 1582)
• March 22 – Johann Carion, German astrologer and chronicler (d. 1537)
• March 31 – Pope Pius IV (d. 1565)^[5]
• May 14 – Agostino Gallo, Italian agronomist (d. 1570)
• June 24 – Johannes Brenz, German theologian and Protestant Reformer of the Duchy of Württemberg (d. 1570)
• July 17 – Maria Salviati, Italian noble and mother of Cosimo I de Medici (d. 1543)
• August 14 – John de Vere, 14th Earl of Oxford, English noble (d. 1526)
• September 3 – Diane de Poitiers, French duchess, mistress of Henry II of France (d. 1566)
• October 13 – Claude of France, queen consort of France, daughter of Louis XII of France (d. 1524)
• October 14 – Catherine of the Palatinate, Abbess of Neuburg am Neckar (d. 1526)
• October 31 – Günther XL, Count of Schwarzburg (1526–1552) (d. 1552)
• November 1 – Rodrigo of Aragon, Italian noble (d. 1512)
• December 8 – Sebald Heyden, German musicologist and theologian (d. 1561)
• December 13 – Justus Menius, German Lutheran pastor (d. 1558)
• date unknown
  • Hans Asper, Swiss painter (d. 1571)
  • Michael Coxcie, Flemish painter (d. 1592)
  • Cesare Hercolani, Italian military leader (d. 1534)
  • Jan Łaski, Polish Protestant reformer (d. 1560)
  • Laurentius Petri, Archbishop of Uppsala (d. 1573)
  • Giulio Romano, Italian painter (d. 1546)
  • Bernardino de Sahagún, Franciscan missionary (d. 1590)
  • Niccolò Fontana Tartaglia, Italian mathematician (d. 1557)
  • Ming, Icelandic clam (d. 2006)^[6]
• probable – Juan Rodríguez Cabrillo, Portuguese explorer (d. 1543)

• January 9 – John Cicero, Elector of Brandenburg (b. 1455)
• March 24 – Edward Stafford, 2nd Earl of Wiltshire, English nobleman (b. 1470)
• April 7 – Galeotto I Pico, Duke of Mirandola (b. 1442)
• August 29 – Alesso Baldovinetti, Florentine painter (b. 1427)
• October 1 – Marsilio Ficino, Italian philosopher (b. 1433)
• November 23 – Perkin Warbeck, Flemish imposter (b. c. 1474) (executed)
• November 28 – Edward Plantagenet, 17th Earl of Warwick, last male member of the English House of York (b. 1475)
• date unknown
  • Rennyo, leader of the Ikko sect of Buddhism (b. 1415)
  • Muhammad Rumfa, ruler of Kano
  • Laura Cereta, Italian humanist and feminist (b. 1469)