During the time of colonization, religious toleration was a concept unheard of within European nations involved. Early Spanish explorers exterminated native religious practices in the Americas they dominated, replacing it with their catholic institutions. Further along the historical timeline of colonization, European countries brought and therefore influenced colonials and natives alike with their religion in occupied areas. As the English grasp upon the new world grew stronger, interesting trends emerged in the American colonies.

Groups fleeing religious persecution in Europe came to the Americas because of the crowns declining influence on colonies that declared total or selective religious toleration and religious regions developed within the new world. Although England was officially Anglican in religion, Puritans, Catholics, and Quakers sought refuge from religious persecution in the English colonies. Puritan separatists and non-separatists fled to the Americas due to opposition to the Church of England's policy on membership and their failed attempt of inhabiting Holland in 1608. Puritans were very strict in religion and this translated into strict governmental policy and structure. The American puritan population concentrated itself in the New England colonies. One specific settlement was the Massachusetts Bay colony containing more liberal Puritans.

Church and government in these puritan settlements were tightly bound together. For instance, voters must be members of the Puritan Church and taxpayers money supported the church. Puritans did not tolerate other's religious beliefs specifically the Quakers. Quakers were fined, flogged, and banished, . If Quakers refused banishment, they were executed.

William Penn, founder of the Pennsylvania colony, launched his colony in 1681. Penn created a colony that suited as a refuge for the Quakers. His fair treatment of Native Americans and ideals of equality drew in the Quakers into his colonies. Pennsylvania was more liberal than the Puritan colonies in that there was no tax supported church. Penns colony was one example of separation of church and state. The Quaker's humane policies meshed well with the progressive principles.

Quakers also thrived in Pennsylvania's neighbors including New Jersey and Delaware. Like the Quakers, Penn's colony accepted Catholics as well. Maryland, founded in 1634 by Lord Baltimore, was created as a Catholic haven. Lord Baltimore allowed freedom of worship within his colonies so that Catholics would not be persecuted. The English were opposed to Catholicism and Lord Baltimore wanted protection of his religious brethren.

Toleration was specifically reserved for only Christian religions, death was the consequence to denying the divinity of Jesus. Although selective, Lord Baltimore's toleration of religion was a progressive concept that founded toleration in modern government. Puritans, Quakers, and Catholics fled European persecution to the English colonies of America. Massachusetts bay colony tolerated the Puritans, Pennsylvania and neighboring regions for Quakers, and Maryland for Catholics. Religious toleration and churches not supported by colonial taxation was the foundation for many aspects of the United States government.