Henry Dunster (1612-1659), the first president of the college at Cambridge (Harvard), had by 1653 become convinced that "visible believers only should be baptized." Being unwilling to hold his views in abeyance, he relinquished in 1654, under circumstances of considerable hardship, the work that he greatly loved.

In 1663 John Myles (1621-1683), a Welsh Baptist who had been one of Cromwell's Tryers, with his congregation, took refuge in Massachusetts from the intolerance of the government of Charles II. They were allowed to settle in Rehoboth, Mass., and even after they were discovered to be Baptists they were allowed to remain on condition of establishing their meeting-place at a considerable distance from that of the standing order. Myles did much to promote the growth of the Baptist Church in Massachusetts, and was of service to the denomination in Boston and elsewhere. Thomas Gould of Charlestown seems to have been in close touch with President Dunster and to have shared his antipaedobaptist views as early as 1654. Some time before 1665 several English Baptists had settled in the neighbourhood of Boston and several others had adopted Baptist views. These, with Gould, were baptized (May 1665) and joined with those who had been baptized in England in a church covenant. The church was severely persecuted, the members being frequently imprisoned and fined and denied the use of a building they had erected as a meeting-house. Long after the Act of Toleration (1689) was in full force in England, the Boston Baptists pleaded in vain for the privileges to which they were thereby entitled, and it required the most earnest efforts of English Baptists and other dissenters to gain for them a recognition of the right to exist.

A mandate from Charles II. (July 1679), in which the Massachusetts authorities were sharply rebuked for denying to others the liberty to secure which they themselves had gone into exile, had produced little effect.

In 1682 William Screven (1629-1713) and Humphrey Churchwood, members of the Boston church, gathered and organized, With the co-operation of the mother church, a small congregation at Kittery, Me. Persecution led to migration, Screven and some of the members making their way to South Carolina, where, with a number of English Baptists of wealth and position, what became the First Baptist church in Charleston, was organized (about 1684). This became one of the most important of early Baptist centres, and through Screven's efforts Baptist principles became widely disseminated throughout that region. The withdrawal of members to form other churches in the neighbourhood and the intrusion of Socinianism almost extinguished the Charleston church about 1746.

A few Baptists of the general (Arminian) type appeared in Virginia from 1714 onward, and were organized and fostered by missionaries from the English General Baptists. By 1727 they had invaded North Carolina and a church was constituted there.

From 1643 onward antipaedobaptists from New England and elsewhere had settled in the New Netherlands (New York). Lady Deborah Moody left Massachusetts for the New Netherlands in 1643 because of her antipaedobaptist views and on her way stopped at New Haven, where she won to her principles Mrs Eaton, the wife of the governor, Theophilus Eaton. She settled at Gravesend (now part of Brooklyn) having received from the Dutch authorities a guarantee of religious liberty. Francis Doughty, an English Baptist, who had spent some time in Rhode Island, laboured in this region in 1656 and baptized a number of converts. This latter proceeding led to his banishment. Later in the same year William Wickenden of Providence evangelized and administered the ordinances at Flushing, but was heavily fined and banished. From 1711 onward Valentine Wightman (1681-1747) of Connecticut (General Baptist) made occasional missionary visits to New York at the invitation of Nicolas Eyres, a business man who had adopted Baptist views, and in 1714 baptized Eyres and several others, and assisted them in organizing a church.

The church was well-nigh wrecked (1730) by debt incurred in the erection of a meeting-house. A number of Baptists settled on Block Island about 1663. Some time before 1724 a Baptist church (probably Arminian) was formed at Oyster Bay.

The Quaker colonies, with their large measure of religious liberty, early attracted a considerable number of Baptists from New England, England and Wales. About 1684 a Baptist church was founded at Cold Spring, Bucks county, Pa., through the efforts of Thomas Dungan, an Irish Baptist minister who had spent some time in Rhode Island. The Pennepek church was formed in 1688 through the labours of Elias Keach, son of Benjamin Keach (1640-1704), the famous English evangelist. Services were held in Philadelphia under the auspices of the Pennepek church from 1687 onward, but independent organization did not occur till 1698. Several Keithian Quakers united with the church, which ultimately became possessed of the Keithian meeting-house. Almost from the beginning general meetings had been held by the churches of these colonies. In 1707 the Philadelphia Association was formed as a delegated body "to consult about such things as were wanting in the churches and to set them in order." From its inception this body proved highly influential in promoting Baptist co-operation in missionary and educational work, in efforts to supply the churches with suitable ministers and to silence unworthy ones, and in maintaining sound doctrine.

Sabbatarianism appeared within the bounds of the association at an early date and Seventh-day Baptist churches were formed (1705 onward).

The decades preceding the "Great Awakening" of 1740-1743 were a time of religious declension. A Socinianized Arminianism had paralysed evangelistic effort. The First Church, Providence, had long since become Arminian and held aloof from the evangelism of Edwards, Whitefield and their coadjutors. The First Church, Boston, had become Socinianized and discountenanced the revival. The First Church, Newport, had been rent asunder by Arminianism, and the nominally Calvinistic remnant had itself become divided on the question of the laying on of hands and showed no sympathy with the Great Awakening. The First Church, Charleston, had been wrecked by Socinianism. The General (Six Principles) Baptists of Rhode Island and Connecticut had increased their congregations and membership, and before the beginning of the 18th century had inaugurated annual associational meetings. But the fact that the Great Awakening in America was conducted on Calvinistic principles was sufficient to prevent their hearty co-operation. The churches of the Philadelphia Association were organized and engaged to some extent in missionary endeavour, but they showed little interest in the Edwards-Whitefield movement. And yet the Baptists ultimately profited by the Great Awakening beyond almost any of the denominations.