The Crusades were a series of military conflicts and wars that was "justified" by religious differences. It was waged by Christians from 1095 to 1291 and was usually sanctioned by the Pope in the name of Christendom, making countries into Christianity based territories. The main goal was the recapturing of Jerusalem and the sacred "Holy Land" from Muslim rule and was originally launched in response to a call from the Eastern Orthodox Byzantine Empire for help against the expansion of the Muslim Seljuq dynasty into Anatolia. The Crusades campaigned through the 16th century in territories outside the Levant and were usually against those that were considered by the Catholic Church to be heretics, a mixture of religious, economic, and political reasons.

The Crusades were an incredibly violent undertaking, even by medieval standards. In its early stages the crusades were less organized but quite bloody. Emich of Leisinged asserted that a cross miraculously appeared on his chest and that certified him for leadership in the Crusades. Before even heading out to kill the enemies of Yahweh, Emich first set out to eliminate the infidels in their midst. His group proceeded to massacre the Jews in German cities like Mainz and Worms and thousands of defenseless men, women and children were chopped, burned or otherwise slaughtered. This type of holy bloodshed was repeated through out Europe by a number of crusading campaigns. Jews however were given a last minute chance to convert to Christianity in accordance with Augustine's doctrines. When Peter the Hermit's army entered Yugoslavia, 4,000 Christian residents of the city of Zemun were massacred before they moved on to burn Belgrade.

As the campaigns began to be led by professional soldiers ordained bishops followed along to bless the atrocities and make sure they had official church approval. Crusaders took the heads of the slain and impaled them upon their weapons. A bishop referred to the impaled heads of the Muslims as a joyful spectacle for the people of Yahweh. It was standard procedure the all the inhabitants, no matter the age, to be killed when Muslim cities were captured by Christian crusaders. St. Bernard announced before the Second Crusade that "The Christian glories in the death of a pagan, because thereby Christ himself is glorified." This sort of tyranny and slaughtering in the name of religion continued on for 196 years.

The Salem Witch Trials of 1692 resulted in a number of convictions and executions for suppose witchcraft in Salem Massachusetts. The trials resulted in the executions of 20 innocent people (14 women, 6 men) and the imprisonment of between 175 and 200 people. In addition to those executed, at least five people died in prison. One man who refused to plead to the charges was pressed to death with rocks.

During the 17th century in Massachusetts most people were Puritans, a very religious group of colonists. They believed that all sins including everything from sleeping in church to stealing food should be punished. When a neighbor would suffer misfortune, such as a sick child or a failed crop, Puritans saw it as Yahweh's will and did not offer help. Puritans also believed that Satan would select the weakest individuals (women, children, the insane) to carry out his work. Those who followed Satan were considered witches and witchcraft was one of the greatest crimes a person could commit, punishable by death as demanded in Exodus 22:18.

European Witch Trials Over a period of 300 years, from 1450 to 1750, 40-60,000 women were accused of witchcraft and put to death due to religious superstition being taken as truth. Even Joan of Arc was suspected of practicing witchcraft although these charges were dropped and she was burned at the stake for other religious heresy convictions.

The French Wars of Religion, (1562 to 1598) were a series of conflicts fought between Catholics and Huguenots (Protestants) from the middle of the sixteenth century to the Edict of Nantes in 1598, including civil infighting as well as military operations. The war was primarily based on religious reasons and involved a struggle for control over the country between the Catholic House of Guise (Lorraine) and the Calvinist House of Bourbon on the other. Hundreds of thousands were killed as a result of this religious conflict.

The Saxon Wars were the campaigns and insurrections of the more than thirty years from 772, when Charlemagne first entered Saxony with the intent to conquer, to 804, when the last rebellion of disaffected tribesmen was crushed. In all, eighteen battles were fought in what is now northwestern Germany to force the monotheistic beliefs of Christianity onto people who had polytheistic religious beliefs.

An inquisition can be run by both civil and church authorities in order to root out non-believers from a nation or religion. The Spanish Inquisition was one of the most deadly inquisitions in history. It was established in 1478 by Catholic Monarchs Ferdinand and Isabella to maintain Catholic orthodoxy in their kingdoms and was under the direct control of the Spanish monarchy. It was not definitively abolished until 1834, during the reign of Isabel II. An estimated 2,000 people were burned at the stake. Over the course of its history, the Inquisition processed a total of 341,021 people, of whom at least 31,912 were executed.

The Reconquista was the seven and a half century long process by which the Christian kingdoms of northern Hispania (modern Portugal and Spain) conquered the Iberian peninsula from the Muslim and Moorish states of Al-Ándalus. The Umayyad conquest of Hispania from the Visigoths occurred during the early 8th century, and the Reconquista is commonly considered to have begun almost immediately in 722, with the Battle of Covadonga, and completed in 1492 with the Conquest of Granada.