? 
"Jews persecuted in Bavaria." [Grun, 244]
1551
Possession of a Bible in any language other than Greek or Latin was a crime in Spain. [Kirsch, 184]
1551
"The Spanish Index of Prohibited Books was first published in 1551...." The Spanish Index was independent from the Vatican's list. It included a number of books which had been approved by Rome. [Johnson, 1976, 307]
1553
Spanish theologian Michael Servetus was burned at the stake for doubting the Trinity. He escaped the Inquisition, only to be captured in Switzerland and burned by Calvin. [Haught, 1990, 90; Cross, 1244; Freeman, 2009, 194-195]
Servetus "had corresponded with Calvin for years and may have hoped to find toleration" of his views by him. Servetus fled the French Inquisition and went to Geneva. Calvin decided to execute him. Protestants as well as Catholics approved. [Engh, 168]
1553-58
Queen Mary I of England ("Bloody Mary"), a Catholic, burned 300 Protestants in three years, as she tried to restore Catholicism using terror. She was a daughter of Henry VIII and the wife of Philip II of Spain. [Haught, 1990, 102; Cross, 870]
1555
The Peace of Augsburg ended war between Holy Roman Emperor Charles V and Protestants led by German Lutheran princes, and "allowed 300 local German rulers to decide whether their districts were to be Catholic or Protestant." The people had to adopt the religion prescribed by their king. It also "recognized the right of Protestant 'heretics' to exist in Germany." [Haught, 1990, 88, 90; Engh, 166]
1555
In England a pregnant woman was burned at the stake for sorcery. She suffered a miscarriage at the stake and her still living baby was thrown back into the flames. [Kirsch, 242]
1555-59
Under Pope Paul IV the inquisition became a reign of terror, killing many "heretics" on mere suspicion. [Haught, 1990, 66]
1556
Church of England official under Henry VIII Thomas Cranmer (b. 1489) was burned at the stake during the reign of the Catholic Mary Tudor. [Grun, 244; Cross, 870]
1556
King Philip II wrote that all the heresies which occurred in Spain, France, and Germany were the work of Jews.[Johnson, 1976, 307]
1558
Scottish Protestant John Knox wrote that every Protestant had a right to kill every Catholic. [Catholic Encyclopedia, "John Knox"]
1559
Many Protestants were burned in Spain in honor of King Philip II, son of Charles V. King Philip, in response to an appeal by a condemned Protestant, "I myself would bring the faggots to burn my own son, were he as perverse as you." [Haught, 1990, 90; Kirsch, 184]
1559
Archbishop of Toledo, Bartolomeo de Carranza, was arrested by the Inquisition and kept in prison for seven years despite papal intervention. [Haught, 1990, 90; Johnson, 1976, 308. See also, 1565 and 1566]
1559
"The first Roman 'Index of Prohibited Books' (Index librorum prohibitorum), published in 1559 under Paul IV, was very severe...." [Catholic Encyclopedia, "Index of Prohibited Books"]
1560
Pope Pius IV ordered that all Protestants in Italy be persecuted. The result was that many men, women and children, of all ages, were killed. [Forbush, VI]
1560
"Beginnings of Puritanism in England." [Grun, 246]
1560
Catholic invaders of the Americas destroyed Mayan temples and idols and burned all Mayan books they found.[Engh, 184]
c.1560
The Inquisition was instituted in Portuguese Goa, at the urging of [St.] Francis Xavier and others. It was not ended until 1812. [Roberts, 89,91]
1561
A yellow smock, which all condemned heretics in Spain had to wear, for each person burned was hung like a trophy in the church where the person had lived. [Kirsch, 201; Johnson, 1976, 307]
1562-89
Catholics and Huguenots in France fought eight wars. [St.] Pope Pius V sent troops to France with orders to take no prisoners. [Haught, 1990, 92, 94]
1562
"1200 French Huguenots slain at Massacre of Vassy; first War of Religion begins." [Grun, 248]
1562
"Diego de Landa burns the libraries of the Maya civilization." [Wikipedia, "Timeline of Christian Missions"]
1565
A papal legation including three future popes, Gregory XIII, Urban VII, and Sixtus V, reported to Pope Pius IV: "Nobody dares to speak in favor of [Archbishop of Toledo] Carranza [see also 1559 and 1566] because of the Inquisition ... and its authority would not allow it to admit that it had imprisoned Carranza unjustly. The most ardent defenders of justice here consider that it is better for an innocent man to be condemned than for the Inquisition to suffer disgrace." [Johnson, 1976, 308]
1565
Spanish Catholic soldiers massacred all members of a Huguenot colony in Florida. [Haught, 1990, 96]
1566
[St.] Pope Pius V finally brought Archbishop Carranza to Rome "where he was held in the fortress of St. Angelo. The power of Spain prevented his clearance until 1576, just eighteen days before his death." [Johnson, 1976, 308; see also, 1559 and 1565]
1568
Spanish King Philip II sent the Duke of Alva to the Netherlands to assist the Inquisition there to persecute Protestants. At one point the Duke condemned the entire population, threatening genocide if they did not submit. There were many massacres by Spanish soldiers, including a mass drowning of about 6000. He also set up what came to be known as the Court of Blood. It condemned 18,000 people to death as heretics. [Stannard, 216; Engh, 169. See also, 1573.]
1568
In Valencia, 2,689 converted Jews confessed to heresy and implicated others in order to avoid torture and burning. [Kirsch, 189]
1571
[St.] Pope Pius V launched the final crusade against Islam. [Haught, 1990, 27]
1572
St. Bartholomew's Day massacre: 10,000 Protestants were killed in France. After the third Catholic/Huguenot war, the Catholic Catherine de Medici had arranged the marriage of a daughter to a Huguenot prince, Henry of Navarre. When Huguenots gathered in Paris for the wedding under a promise of safe passage, Catherine plotted with Catholic dukes to assassinate the Huguenot military leader, Admiral Gaspard de Coligny. The assassin missed, merely wounding the admiral-so Catherine and the dukes hastily decided to murder all the Huguenots before they had time to counterattack. On St. Bartholomew's Day Catholic troops swept through Huguenot neighborhoods in Paris, slaughtering thousands. Admiral Coligny was beheaded. Other massacres were staged throughout France.
Coligny's head was sent to Rome, where Pope Gregory XIII received it joyfully. He wrote to France's Charles IX, "We rejoice with you that with the help of God you have relieved the world of these wretched heretics." He and the whole college of cardinals offered a mass of thanksgiving. The pope struck a medal celebrating the Catholic victory and commissioned the artist Giorgio Vasari to paint a fresco of the triumph. The massacre triggered another war and four more followed. Finally, Henry of Navarre was offered the crown as king of France if he would convert to Catholicism. He did so. [Haught, 1990, 94, 96; Ellerbe, 95]
1573
The Duke of Alva massacred Haarlem Protestants. The duke also killed thousands in Antwerp. He was sent by King Philip II, ruler of Holland and Belgium, to kill all Protestants after they had rebelled and burned 400 Catholic churches. Philip also revived the Inquisition. [Haught, 1990, 98, 100. See also, 1568]
1574
"First auto-da-fé in Mexico." [Grun, 254]
1574
The Spanish government waged war against the Chichimeca in the Mexican state of Michoacán. [Wikipedia, "Timeline of Christian Missions"]
1575
The Spanish Inquisition in Seville imprisoned an Englishman for seven years for possession of a Protestant prayer book. [Kirsch, 184]
1577
"Dominicans enter Mozambique and penetrate inland, burning Muslim mosques as they go. [Wikipedia, "Timeline of Christian Missions"]
1578
Inquisitor Francisco Pena stated, "We must remember that the main purpose of the trial and execution is not to save the soul of the accused but to achieve the public good and put fear into others." [Ellerbe, 76; Kirsch, 189-190]
1578
"King of Spain orders the bishop of Lima not to confer Holy Orders on mestizos." [Wikipedia, "Timeline of Christian Missions"]
1580
The Inquisition in Goa disinterred and burnt the remains of Garcia d'Orta, a noted physician. Inquisitors did this to dead Jews who had not been condemned while they were alive. [Stannard, 209]
1581
Jesuit Edmund Campion was tortured and executed for treason in England. He converted from the Church of England to Catholicism, preaching and publishing pamphlets. [Cross, 225; Grun, 256]
1581
"... Pope Gregory XIII forbade Jews to employ Christian wet-nurses because of the slander ... that Jews make these women pour their milk into the latrines for three days [after taking communion] before they again give suck to the children." [Kirsch, 170-171]
1583
In Vienna, a 16-year-old girl suffered stomach cramps. Jesuits exorcised her for 8 weeks. Her grandmother was tortured into confessing she was a witch, then burned at the stake. "One of perhaps one million such executions during three centuries of witch hunts." [Haught, 1990, 10]
1584
William of Orange was killed after leading Dutch Protestants in a rebellion against Catholic Spain. [Haught, 1990, 100]
1586
"... the entire female population of two villages was wiped out by the inquisitors, except for only two women left alive." [Ellerbe, 136]
1587-93
Archbishop Johann von Schoneburg burned more than 300 "witches" in twenty-two villages around Trier. He also tortured, strangled and burned the chief judge of the electoral court, a university rector, for leniency. [Johnson, 1976, 310]
1590
Philip II proclaimed that witchcraft was "the scourge of the human race." [Johnson, 1976, 310]
Late 1500s
879 heresy trials were recorded in Mexico. The Inquisition had been brought to the Americas by Spaniards to punish Indians who reverted to native religions. [Haught, 1990, 66; Stannard, 218]
1598
After Henry of Navarre had assumed the French throne as Henry IV, he issued the Edict of Nantes, which permitted French Huguenots (Protestants) to worship freely. "When the Edict of Nantes was signed in 1598 it was promptly denounced by Pope Clement VIII as 'the worst thing in the world'." [Johnson, 1976, 319]