Prior to the Judeo-Christian religious tradition, and still in many Eastern countries, no distinction was made between worldly or secular authority and religious or spiritual authority. In the pagan Roman Empire, rulers (Emperors or Caesars) were considered gods, so the state was worshiped as both an earthly and heavenly power. Both Jews and early Christians refused to worship the king as they considered him a false god, and they were persecuted as a consequence. Church members in the Roman Empire were often forced to light candles and bow down to government officials and if they refused, were put to death. The emperor Nero killed thousands of Christians who refused to worship him.

With Emperor Constantine I, Christianity became first a legal, accepted religion and then the official religion of the Roman Empire (A.D. 330). The correct relationship of religion and government was addressed by several prominent Christian theologians, including St. Augustine, St. Thomas Aquinas, Martin Luther, and John Calvin.

In the Catholic teaching (Augustine and Aquinas), the church and state are separate but related, the former primarily concerned with spiritual teaching and worship and the latter with police functions and military defense. Because just laws require moral knowledge and religion is the source of morality, the church must advise the government on secular legal matters. Ultimately, if the society and the church have a conflict over a public issue, the church should prevail because it is closer to God. This led to the Roman Catholic Church and its leader, the pope, dictating laws to European monarchs.

Emperor Charlemagne (800-814) challenged this church supremacy in politics when he began to appoint bishops himself. This culminated in Pope Gregory VII's ban on such "lay investiture" of Catholic bishops in 1073. The Protestant Reformation modified the Catholic view of church-state relations. Martin Luther claimed that the government had supreme authority in social matters and that the church should be primarily concerned with spiritual matters and the individual's "inner life." John Calvin saw a shared rule of society by government and religious leaders. This caused German Protestant princes to assume legal authority over the church, an idea later adopted by King Henry VIII in England.

With the proliferation of separate, dissenting Protestant churches in England and America, the idea of toleration of various sects and freedom of religious belief expanded. This reached its height in the United States, where individual religious belief and freedom is protected by the Constitution. This reflects the idea of separation of church and state. The U.S. Supreme Court decides the relationship of religion and politics, including prayer in public schools, rights of religious expression and employment, and spiritual education. Constitutional law is complex, but it tries to steer a line between the two First Amendment clauses that govern church-state relations in the United States. The "establishment clause" states that the federal government shall not make laws respecting an establishment of religion, that is, an official state church (as the Church of England); the "free exercise" clause says that Congress shall not make a law violating the free exercise (belief, expression, etc.) of an individual's religion. Protecting one of the clauses (such as avoiding public support of religion by permitting prayer in schools) may harm the other clause rights (punishing those who want to express their religion by praying in school). The Supreme Court has tried to strike a balance between these two, avoiding entanglement with government in religion and not persecuting religious people. So, for example, in various rulings it has held that students may not pray (led by a school official) during regular school hours in the school building but may pray together as a group or club in the building before or after regular school hours.

The primary motivation of religious freedom in America was to keep the government out of regulating church affairs (doctrine, liturgy, worship, polity, etc.). Early American Baptists, especially in Virginia, fought for noninterference of the state in church matters, resulting in Thomas Jefferson's statute for religious freedom. But American Christians continued to believe that state laws required moral knowledge to be just, and moral knowledge required religious influence in the government. The hope of Evangelical Christians was that religious liberty would create widespread conversions to Christianity and that a generally Christian culture would make Godly laws and policy.

As the United States became more pluralistic (with non-Western, non-Christian inhabitants) as well as more liberal politically, this evangelical expectation of a Christian America was disappointed. By the 1950s, U.S. society became less and less recognizably Christian in culture. An attempt to restore the earlier religious atmosphere in the United States was made by the Christian Right in passing laws conforming to religious sensibilities (limited divorce, restricting abortion, allowing prayer in school, etc.). The dynamic between church and state promises to continue to be an active feature of U.S. culture in the future.

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