Colonization of New England was due to the fact that in England, Puritans called Congregationalists wanted to reform the church. Other Puritans called Separatists thought the church was already too corrupt and could not be saved. To get the religious freedom they longed for and open their lives to new opportunity, the Separatists established a settlement in New England. Since people were being persecuted in Europe, especially in England, because of their religion, religious groups such as the Puritans flocked to the New World (more specifically, Massachusetts Bay). This represented a paradox, however, in that from fleeing the royal wrath intolerant of their religion, these Pilgrims (who were the purest of the Puritans) did not tolerate other religions in their colony.

However, as the population for the British North American colonies increased, so did religious tolerance, especially in other colonies. In building the Bay Colony, the Puritans incorporated religion into their political ideals. Thus, Massachusetts was dubbed "the Blue Law State". Unchurched men were deemed voteless, as were women. Naturally, there would be dissenters among these settlers. Those who dissented from the Puritans' "moral righteousness" were banished or killed.

The Puritans believed they were right in doing this, because they were "divinely favored" by God. The Puritans also believed that their lives were a "divine mission" to settle the "city upon a hill" (Massachusetts). However, some dissenters disagreed and felt that church and state should be separate. In a letter to Major John Mason, a man named Roger Williams noted "forced worship stinks in God's nostrils".

Roger Williams said that government should not regulate religious behavior, and that the Pilgrims should break their ties with the Church of England. He was ultimately banished for his views, and fled to Rhode Island. There, he founded Rhode Island in 1636 to be a very liberal and religiously tolerant colony. In the same year, The Royal Charter for the colony of Rhode Island was obtained from King Charles II by Dr. John Clarke.

The charter guaranteed religious freedom, and Rhode Island was established as a self-governing colony. As a result, many French Huguenots and Catholics settled in Massachusetts. Another haven for Catholics would later become Maryland. Founded by Lord Baltimore in 1634, Maryland later passed the Act of Toleration (1649) in which all Christians were granted religious freedom. Further south however, many colonies were still controlled by the Anglican Church.

In the late 17th century, a man by the name of William Penn wanted to found a colony that tolerated Quakers. In 1681, Penn received a grant for land from England. This land was the best advertised of all the colonies, and consequentially, more and more people from the Old World flocked over to settle in Pennsylvania. William Penn especially welcomed carpenters, masons, and manual workers. Penn's colony was also formally launched that same year. It became the most liberal and religiously tolerant of all the colonies.

Although the colonies would later unite to become one nation, they shared many differences (especially on the views of religion) in their early years. This made for a diverse population in the British North American colonies, as strict Puritans inhabited Massachusetts, French Huguenots settled in Rhode Island, Catholics in Maryland, and Quakers in Pennsylvania. As time wore on however and populations increased, each colony became more and more religiously tolerant, thus making the 13 colonies a mixing pot for different races and religion.