2000 years of history has some lessons

Early Christianity was a minority religion in the Roman Empire and the early Christians were themselves persecuted during that time. After Constantine I converted to Christianity, it became the dominant religion in the Roman Empire. Already beginning under his reign, Christian heretics were persecuted; The most extreme case (as far as historians know) was the burning of Priscillian and six of his followers at the stake in 383. In the view of many historians, the Constantinian shift turned Christianity from a persecuted into a persecuting religion Beginning in the late 4th century A.D. also the ancient pagan religions were actively suppressed.

After the decline of the Roman Empire, the further Christianization of Europe was to a large extent peaceful, although Jews and Muslims were harshly prosecuted, to an extent of forced conversions to Christianity in Byzantine empire. Encounters between Christians and Pagans were sometimes confrontational, and some Christian kings (Charlemagne, Olaf I of Norway) were known for their violence against pagans. The persecution of Christian heretics resumed in 1022, when fourteen people were burned at Orléans. Around this time Bogomilism and Catharism appeared in Europe; these sects were seen as heretic by the Catholic Church, and the Inquisition was initially established to counter them. Heavily persecuted, these heresies were eradicated by the 14th century. The suppression of the Cathar (or "Albigensian") faith took the form of the Albigensian Crusade (1209–1229), a 20-year military campaign initiated by the Roman Catholic Church. Its violence was extreme even by medieval standards. Notable individuals who were executed for heresy in the late Middle Ages are Jerome of Prague, John Badby and Jan Hus. Only the Waldensians, another heretical Christian sect, managed to survive in remote areas in Northern Italy.

Also during the late Middle Ages, the Crusades pitched Christians and Muslims against each other in a war about the possession of Jerusalem, with atrocities from both sides. There were massacres of Muslims and Jews when Jerusalem was taken by Crusaders in 1099. There were also the Northern Crusades, against the remaining pagans in Northern Europe. As a result, the pagan religions in Europe disappeared almost completely. After Grand Duchy of Moscow and later the Tsardom had conquered the Kazan Khanate and Astrakhan Khanate in the 1550s, the government forcibly baptized Muslim Volga Tatars and pagan Chuvash, Mordva and Mari. Mosques were prohibited. This persecution ended only under the reign of Catherine II of Russia in the late eighteenth century.

The Spanish and Portuguese Inquisition also went on to persecute Jews and Muslims. In Spain after the Reconquista, Jews were forced to either convert or be exiled. Many were killed. The persecution of Jews goes back to 12th century Visigothic Spain after the emergence of the blood libel against Jews. Although the Spanish had agreed to allow Muslims the freedom of religion in 1492, this was often ignored. In 1501, Muslims were offered the choice of conversion or exile. In 1556, Arab or Muslim dress was forbidden, and in 1566 Arabic language as a whole was prohibited in Spain.[5] Jews were eventually expelled from England by King Edward I, too.

When Martin Luther wrote his Ninety-Five Theses in 1517, Catholicism reacted the same way as it had to the heresies of the late Middle Ages. However, while the Protestant Reformation could be "crushed" in Spain with "a few dozen executions in the 1550s",[6] the same strategy failed in Germany, Northern Europe and in England. France had to suffer through the French Wars of Religion before it again became wholly Catholic. The divide between Catholicism and the new Protestant denominations was deep. Protestants commonly alleged that the catholic Pope was the Antichrist. Conflicts between Christian factions reached their heights in France with the 1572 St. Bartholomew's Day Massacre, in Germany and Central Europe with the Thirty Years' War (1618–1648) and in England with the English Civil War (1641–1651). Following the devastations caused by these wars, the ideas of religious toleration, freedom of religion and religious pluralism slowly gained ground in Europe. The Witch trials in Early Modern Europe, which had reached their height between 1550 and 1650, continued until 1750.

European Colonialism, that was accompanied by Christian evangelism and often by violence, led to the suppression of indigenous religions in the territories conquered or usurped by the Europeans. The Spanish colonization of the Americas largely destroyed the Aztec and Inca civilization. However, Colonialism (and later European Imperialism) as a whole were not motivated by religious zeal; the suppression of the indigenous religions was their side result, not their main purpose. Only partial aspects, like the Goa Inquisition, bear resemblance to the persecutions that occurred on the European continent. By the 18th century, persecutions of unsanctioned beliefs had been reduced in most Europeans countries to religious discrimination, in the form of legal restrictions on those who did not accept the official faith. This often included being barred from higher education, or from participation in the national legislature. In colonized nations, attempts to convert native peoples to Christianity became more encouraging and less forceful. In British India during the Victorian era, Christian converts were given preferential treatment for governmental appointments.