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In 1559, a number of clergymen returned to England from exile in Europe. They were members of the Church of England, who had taken refuge there to escape the persecution of Protestants in Queen Mary's reign. Mary had rejected the reformation of the church that had taken place under her father, Henry VI11. She wanted to restore the English church to the folds of Roman Catholicism, and to enforce her wishes she had burned those people who opposed her. With her death and the ascension to the throne of Elizabeth, a Protestant, many of the exiled clergy returned from their European refuges. They brought with them new patterns of belief which they had learned from their Continental friends, especially John Calvin in Geneva and Martin Bucer in Strasbourg. These emphases distinguished them from the rest of the clergy and became the earliest hallmarks of the Puritan movement.

The word Puritan means 'would-be reformer'; the returning exiles wanted to see the Church of England thoroughly reformed. Theologically, they would accept nothing as binding on the church that was not proved from the pages of Scripture. What was not demanded by the Bible could not be made mandatory on the conscience of an individual Christian without attacking the idea of Christian liberty.

Politically, the Puritans did not want the reformation of the church to be in the hands of the secular authorities. Instead, they demanded that the sole and final authority for the ordering of the church should be in the hands of the church's own officers.

Queen Elizabeth was sympathetic to the Protestant cause. Yet she was convinced that she herself must govern the church directly, because it was too powerful an institution to be left in hands that might not support her. And so she forced two Acts of Parliament to be passed. The first was the Act of Supremacy, which established the monarch as the head of the Church of England, and vested in her the power to rule and reform the church. The second was the Act of Uniformity, which required that all Englishmen should give religious obedience to the established Church of England. This obedience involved accepting the 'episcopal' form of government (bishops, priests and deacons) and also the set liturgical forms of worship.

The history of the Puritan protest movement falls into three periods, each period with specific demands for change, and each producing its own leaders:

-From Queen Elizabeth's ascension to the throne until the crushing of the Presbyterian movement in 1593;

-From the revival of the movement in 1593 until 1640, when the Long Parliament was called in Charles I's time;

-From 1640 through the period of Cromwell and Puritan ascendancy until 1660, with Charles II's return, the Restoration and the ejection of Puritan clergy from their positions.

The Puritans made an early impact on American history, through the Pilgrim Fathers, who were concerned to set up a godly community under the rule of the Bible.

The initial principles of Puritanism were brought from Geneva and Zurich where the majority of the exiles had been given shelter. One of the first things they learned was to disdain the outward show of religion. On their return, the exiles found themselves in bitter opposition to the clergy wearing vestments, especially the surplice. But their objections were much more fundamental than simply refusing to dress up for church services. They were concerned that the reformation within the Church of England had not gone nearly far enough. As they saw it, Elizabeth was not prepared for a really thorough-going reform; she wanted only to preserve her own control of the church.

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