The history of Christian thought has included concepts of both inclusivity and exclusivity from its beginnings. These have been understood and applied differently in different ages, and have led to practices of both persecution and toleration. Early Christian thought established Christian identity, defined heresy and orthodoxy, and separated itself from polytheism and Judaism. Nearly all scholars prior to the late twentieth century claimed Christian thought was intolerant, as evidenced by the persecution of pagans and violence in the centuries after Christianity became favored by Christian emperors in the Roman Empire. However, the majority of modern scholars say that the change to Christian leadership did not cause the persecution of pagans, and that violence in society did not increase.Cameron, A. 1991. Christianity and the Rhetoric of Empire. London. 121-4Markus, R. 1991. The End of Ancient Christianity. Cambridge.Trombley, F. R. 1995a. Hellenic Religion and Christianisation, c. 370–529. New York. I. 166-8, II. 335-6

After the fall of the Roman Empire, Christian thought focused more on preservation than origination. This era of thought is exemplified by Gregory the Great, Saint Benedict, Visigothic Spain, illustrated manuscripts, and progress in medical care through monks. Although the roots of supersessionism, the theory that Christians replaced Jews as God's chosen, and deicide can be traced to some second century Christian thought, Jews of the Middle Ages lived mostly peacefully alongside their Christian neighbors because of Augustine of Hippo's teaching that they should be left alone. In the Early Middle Ages, Christian thought on the military and involvement in war shifted to accommodate the crusades by inventing chivalry and new monastic orders dedicated to it. There was no single thread of Christian thought throughout most of the Middle Ages, as the Church was largely democratic and each order had its own doctrine.

The High Middle Ages were pivotal in both European culture and Christian thought. Feudal kings began to lay the foundation of what would become their modern nations by centralizing power. They gained power through multiple means including persecution. Christian thought played a supportive role, as did the literati, a group of ambitious intellectuals who had contempt for those they thought beneath them, by verbally legitimizing those attitudes and actions. This contributed to a turning point in Judeo-Christian relations in the 13th century. Heresy became a religious, political, and social issue which led to civil disorder and the Medieval Inquisitions. The Albigensian Crusade is seen by many as evidence of Christianity's propensity for intolerance and persecution, while other scholars say it was conducted by the secular powers for their own ends.

The Late Middle Ages are marked by a decline in papal power and church influence, with accommodation to secular power becoming an increasingly prominent aspect of Christian thought. The modern Inquisitions were formed in the Late Middle Ages at the special request of the Spanish and Portuguese sovereigns. Where the medieval inquisitions had limited power and influence, the powers of the modern "Holy Tribunal" were taken over, extended, and enlarged by the state into "one of the most formidable engines of destruction which ever existed." During the Northern Crusades, Christian thought on conversion shifted to a pragmatic acceptance of conversion obtained through political pressure or military coercion even though theologians of the period continued to write that conversion must be voluntary.

By the time of the early Reformation (1400–1600), the conviction developed among the early Protestants that pioneering the concepts of religious freedom and religious toleration was necessary. Scholars say tolerance has never been an attitude broadly espoused by an entire society, not even western societies, and that only a few outstanding individuals, historically, have truly fought for it. In the West, Christian reformation figures, and later Enlightenment intellectuals, advocated for tolerance in the century preceding, during, and after the Reformation and into the Enlightenment. Contemporary Christians generally agree that tolerance is preferable to conflict, and that heresy and dissent are not deserving of punishment.

Early Christian thought from the first century to Constantine Historical background In its first three centuries, Christian thought was just beginning to define what it meant to be a Christian, distinct from paganism and Judaism, through its definitions of orthodoxy and heterodoxy. Early Christian writers worked to reconcile the Jewish founding story, the Christian gospel of the Apostles, and the Greek tradition of knowing the divine through reason, but the substance of Christian orthodoxy was increasingly found in the homogeneous canon of writings believed to be apostolic (written by the apostles), that had circulated widely as such, and the writings of the Church Fathers that were based on them.

Persecution and tolerance are both the result of alterity, the state of otherness, and the question of how to properly deal with those who are 'outside' the defined identity. Like the other Abrahamic religions, Christian thought has included, from its beginnings, two ideals which have affected Christian responses to alterity: inclusivity (also called universality) and exclusivity, or as David Nirenberg describes them, our "mutual capacities for coexistence and violence."Nirenberg, David. Communities of Violence: Persecution of Minorities in the Middle Ages Updated Edition. United Kingdom, Princeton University Press, 2015. There is an inherent tension in all the Abrahamic traditions between exclusivity and inclusivity, which is theologically and practically dealt with by each in different ways.Hastings, Ed. The Oxford Companion to Christian Thought. United Kingdom, Oxford University Press, US, 2000.

Justo L. González traces three veins of Christian thought that began in the second century. Out of Carthage, Tertullian the lawyer (155–200 CE) wrote of Christianity as a revelation of the law of God. From the pluralistic city of Alexandria, Origen wrote of the commonalities between philosophy and theology, reason and revelation, seeing Christianity as the intellectual pursuit of transcendent truth. In Asia Minor and Syria, Irenaeus saw Christianity as God working in human history through its pastoral work of bringing people into God's love. Each vein of thought has persisted throughout Christian history and has shaped attitudes toward and practices of tolerance and persecution.

Inclusivity, exclusivity and heresy Early Christian communities were highly inclusive in terms of social stratification and other social categories, much more so than were the Roman voluntary associations. Heterogeneity characterized the groups formed by Paul the Apostle, and the role of women was much greater than in either of the forms of Judaism or paganism in existence at the time. Early Christians were told to love others, even enemies, and Christians of all classes and sorts called each other "brother" and "sister". These concepts and practices were foundational to early Christian thought, have remained central, and can be seen as early precursors to modern concepts of tolerance.

Though tolerance was not a fully developed concept, and was held with some ambivalence, Guy Stroumsa says Christian thought of this era promotes inclusivity, yet invents the concept of heresy at the same time. Tertullian, a second-century Christian intellectual and lawyer from Carthage, advocated for religious tolerance primarily in an effort to convince pagan readers that Christianity should be allowed into the religious "market-place" that historian John North proposes second century Rome had become. On the other hand, Stroumsa argues that Tertullian knew co-existence meant competition, so he attempted to undermine the legitimacy of the pagan religions by comparing them to Christianity at the same time he advocated for tolerance from them. Justin Martyr (100–165 CE) wrote his First Apology (155–157 CE) against heretics, and is generally attributed with inventing the concept of heresy in Christian thought. Historian Geoffrey S. Smith argues that Justin writes only to answer objections his friends are facing and to defend these friends from ill treatment and even death. He quotes Justin in a letter to Emperor Antoninus Pius as saying he is writing: "On behalf of those from every race of men who are unjustly hated and ill-treated, being one of them myself." However, Alain Le Boulluec argues it is within this period that use of the term "heretic" in Christian thought and writings changes from neutral to derogatory.

Supersessionism

Supersessionist thought is defined by "two core beliefs: (1) that the nation of Israel has forfeited its status as the people of God through disobedience; and (2) the New Testament church has therefore become the true Israel and inheritor of the promises made to the nation of Israel." It has three forms: punitive, economic, and/or structural supersessionism. Punitive supersessionism is the 'hard' form of supersessionism, and is seen as punishment from God of Jews. Economic supersessionism is a more moderate form concerning God's economy: His plan in history to transfer the role of the "people of God" from an ethnic group to a universal group. The third form involves the New Testament taking priority over the Old Testament (Hebrew Bible) and ignoring or replacing the original meaning of Old Testament (Hebrew Bible) passages. For example, within the early church, the rise of the use of Greek philosophical interpretation and allegory allowed inferences to be drawn such as the one Tertullian drew when he allegorically interpreted the statement "the older will serve the younger", concerning the twin sons of Isaac and Rebekah (Genesis 25:23), to mean that Israel would "serve" the Church.

There is no agreement on when supersessionism began. Michael J. Vlach notes that some claim it began in the New Testament; some say it began with the Church Fathers; and others place its beginnings after the Bar Kokhba revolt in 135 CE. The 70 CE siege of Jerusalem and the destruction of the Second Temple, and the later Bar Kokhba revolt, both had a profound impact on Jewish–Christian relations. Many saw the still-extant Jewish Christians as traitors for not supporting their non-Christian Jewish kinfolk, and Vlach says supersessionism grew out of those events. Scholars such as Walter Kaiser Jr. see the fourth century, after the ascension of Constantine the Great, as supersessionism's true beginning, because that is when a shift in Christian thought on eschatology took place. The early Church reinterpreted Revelation 20:4–6—and its hope for a millennial reign of Jesus with a "redeemed" Israel after his Second Coming—and replaced it with a "historicized and allegorized version" that positioned the Church as the metaphorical Israel instead.