Religious persecution is the systematic oppression of an individual or a group of individuals as a response to their religious beliefs or affiliations or their lack thereof. The tendency of societies or groups within societies to alienate or repress different subcultures is a recurrent theme in human history. Moreover, because a person's religion frequently determines his or her sense of morality, worldview, self-image, attitudes towards others, and overall personal identity to a significant extent, religious differences can be significant cultural, personal, and social factors. Religious persecution may be triggered by religious or antireligious stances (when members of a dominant group denigrate religions other than their own or religion itself where the irreligious are the dominant group) or it may be triggered by the state when it views a particular religious group as a threat to its interests or security. At a societal level, the dehumanization of a particular religious group may readily lead to acts of violence or other forms of persecution. Religious persecution may be the result of societal and/or governmental regulation. Governmental regulation refers to the laws which the government imposes in order to regulate a religion, and societal regulation is discrimination against citizens because they adhere to one or more religions. In many countries, religious persecution has resulted in so much violence that it is considered a human rights problem.

David T. Smith, in Religious Persecution and Political Order in the United States, defines religious persecution as "violence or discrimination against members of a religious minority because of their religious affiliation," referring to "actions that are intended to deprive individuals of their political rights and force minorities to assimilate, leave, or live as second-class citizens. In the aspect of a state's policy, it may be defined as violations of freedom of thought, conscience and belief which are spread in accordance with a systematic and active state policy which encourages actions such as harassment, intimidation and the imposition of punishments in order to infringe or threaten the targeted minority's right to life, integrity or liberty. The distinction between religious persecution and religious intolerance lies in the fact that in most cases, the latter is motivated by the sentiment of the population, which may be tolerated or encouraged by the state. The denial of people's civil rights on the basis of their religion is most frequently described as religious discrimination, rather than religious persecution.

Examples of persecution include the confiscation or destruction of property, incitement of hatred, arrests, imprisonment, beatings, torture, murder, and executions. Religious persecution can be considered the opposite of freedom of religion.

Bateman has differentiated different degrees of persecution. "It must be personally costly... It must be unjust and undeserved... it must be a direct result of one's faith."

From a sociological perspective, the identity formation of strong social groups such as those which are generated by nationalism, ethnicity, or religion, is a causal aspect of practices of persecution. Hans G. Kippenberg [de] says that it is these communities, which can be a majority or a minority, that generate violence. Since the development of identity involves 'what we are not' as much as 'what we are', there are grounds for the fear that tolerance of 'what we are not' can contribute to the erosion of identity. Brian J. Grim and Roger Finke say that the perception that plurality is dangerous leads to religious persecution. Both the state and any dominant religion, share the concern that to "leave religion unchecked and without adequate controls will result in the uprising of religions that are dangerous to both state and citizenry," and this concern gives both the dominant religion and the state motives for restricting religious activity. Grim and Finke say it is specifically this religious regulation that leads to religious persecution. R.I. Moore says that persecution during the Middle Ages "provides a striking illustration of the classic deviance theory, [which is based on identity formation], as it was propounded by the father of sociology, Émile Durkheim". Persecution is also, often, part of a larger conflict involving emerging states as well as established states in the process of redefining their national identity.

James L.Gibson adds that the greater the attitudes of loyalty and solidarity to the group identity, and the more the benefits to belonging there are perceived to be, the more likely a social identity will become intolerant of challenges. Combining a strong social identity with the state, increases the benefits, therefore it is likely persecution from that social group will increase. Legal restriction from the state relies on social cooperation, so the state in its turn must protect the social group that supports it, increasing the likelihood of persecution from the state as well. Grim and Finke say their studies indicate that the higher the degree of religious freedom, the lower the degree of violent religious persecution. "When religious freedoms are denied through the regulation of religious profession or practice, violent religious persecution and conflict increase."

Perez Zagorin writes "According to some philosophers, tolerance is a moral virtue; if this is the case, it would follow that intolerance is a vice. But virtue and vice are qualities solely of individuals, and intolerance and persecution [in the Christian Middle Ages] were social and collective phenomena sanctioned by society and hardly questioned by anyone. Religious intolerance and persecution, therefore, were not seen as vices, but as necessary and salutary for the preservation of religious truth and orthodoxy and all that was seen to depend upon them." This view of persecution is not limited to the Middle Ages. As Christian R. Raschle and Jitse H. F. Dijkstra, say: "Religious violence is a complex phenomenon that exists in all places and times."

In the ancient societies of Egypt, Greece and Rome, torture was an accepted aspect of the legal system. Gillian Clark says violence was taken for granted in the fourth century as part of both war and punishment; torture from the carnifex, the professional torturer of the Roman legal system, was an accepted part of that system. Except for a few rare exceptions, such as the Persian empire under Cyrus and Darius, Denis Lacorne says that examples of religious tolerance in ancient societies, "from ancient Greece to the Roman empire, medieval Spain to the Ottoman Empire and the Venetian Republic", are not examples of tolerance in the modern sense of the term.