In 1660, when news of the restoration of the monarchy in England reached the colonies, Connecticut's General Court, aware that the new king, Charles II, was not a big fan of Congregationalists, became concerned about the fact that their colony had never been granted an official charter. A charter was quickly drafted, and the colony's governor, John Winthrop, Jr., sailed to England to present it to the Privy Council. Winthrop's mission was successful, and the charter was officially adopted by the General Court on October 9, 1662. Although this charter had almost no effect on the existing government of Connecticut, it is considered by some to be the state's second constitution.

Around the time of the American Revolution, all of the states, with the exception of Connecticut and Rhode Island, adopted state constitutions. These constitutions, written at the suggestion of the Continental Congress, were necessary because these states would need new governments once they were independent from England. Connecticut and Rhode Island, however, both of which already had functioning governments that would not be affected when ties to England were severed, saw no need to write state constitutions at this time. In 1776, the Connecticut General Assembly (formerly the General Court) declared:

That the ancient form of civil government contained in the Charter from Charles the II, King of England, and adopted by the people of this state, shall be and remain the civil constitution of this state, under the sole authority of the people hereof, independent of any king or prince whatever.

So, with the exception of deleting any references to England in the Charter, there was no change to the government of Connecticut.

By 1800, all of the other states had made significant progress towards religious freedom. Not every state had the liberal freedom enjoyed in states like Pennsylvania and Virginia, but none had the degree of religious discrimination practiced in Connecticut. The Congregationalist government of Connecticut, established by the Fundamental Orders in 1638-1639, legitimized by the Charter of 1662, and left unchanged at the time of the Revolution, was the government that still existed on October 7, 1801, when the Danbury Baptist Association wrote the following letter to President Thomas Jefferson.

Sir, Among the many million in America and Europe who rejoice in your election to office; we embrace the first opportunity which we have enjoyed in our collective capacity, since your inauguration, to express our great satisfaction, in your appointment to the chief magistracy in the United States: And though our mode of expression may be less courtly and pompous than what many others clothe their addresses with, we beg you, sir, to believe that none are more sincere.

Our sentiments are uniformly on the side of religious liberty-that religion is at all times and places a matter between God and individuals-that no man ought to suffer in name, person, or effects on account of his religious opinions-that the legitimate power of civil government extends no further than to punish the man who works ill to his neighbors; But, sir, our constitution of government is not specific. Our ancient charter together with the law made coincident therewith, were adopted as the basis of our government, at the time of our revolution; and such had been our laws and usages, and such still are; that religion is considered as the first object of legislation; and therefore what religious privileges we enjoy (as a minor part of the state) we enjoy as favors granted, and not as inalienable rights; and these favors we receive at the expense of such degrading acknowledgements as are inconsistent with the rights of freemen. It is not to be wondered at therefore; if those who seek after power and gain under the pretense of government and religion should reproach their fellow men-should reproach their order magistrate, as a enemy of religion, law, and good order, because he will not, dare not, assume the prerogatives of Jehovah and make laws to govern the kingdom of Christ.

Sir, we are sensible that the president of the United States is not the national legislator, and also sensible that the national government cannot destroy the laws of each state; but our hopes are strong that the sentiments of our beloved president, which have had such genial effect already, like the radiant beams of the sun, will shine and prevail through all these states and all the world, till hierarchy and tyranny be destroyed from the earth. Sir, when we reflect on your past services, and see a glow of philanthropy and good will shining forth in a course of more than thirty years we have reason to believe that America's God has raised you up to fill the chair of state out of that goodwill which he bears to the millions which you preside over. May God strengthen you for your arduous task which providence and the voice of the people have called you to sustain and support you enjoy administration against all the predetermined opposition of those who wish to raise to wealth and importance on the poverty and subjection of the people.

And may the Lord preserve you safe from every evil and bring you at last to his heavenly kingdom through Jesus Christ our Glorious Mediator.

Signed in behalf of the association,

Nehemiah Dodge Ephraim Robbins Stephen S. Nelson

According to D. James Kennedy, in his book What If America Were A Christian Nation Again?:

"...Late in 1801, while he was president, he received a letter from the Association of Baptists in Danbury, Connecticut, who were concerned about the threat of the newly formed federal government. This `leviathan,' they feared, could become a great danger to their Christian faith and to their churches."

"...On the first day of the year 1802, Jefferson wrote back to the Danbury Baptists. In this letter, he said that he was greatly impressed that the American people, through the First Amendment had, in effect, erected a `wall of separation between the church and the state,' so the Baptists didn't need to fear that the federal government was going to intrude upon their religion or in any way disturb their faith."

According to William Federer, in his book America's God and Country Encyclopedia of Quotations:

"On January 1, 1802, Jefferson wrote a letter to the Danbury Baptist Association of Danbury, Connecticut, calming their fears that Congress was not in the process of choosing any one single Christian denomination to be the `state' denomination, as was the case with the Anglican Church in England and Virginia...."

"...This personal letter reassured the Baptists that the government's hands were tied from interfering with, or in any way controlling, the affairs or decisions of the churches in America."

The biggest myth about this letter is the Baptists wrote it because they feared that the federal government planned to establish a national religion, a notion that is ridiculous for several reasons. The most obvious of these is that the letter refers only to the problem in Connecticut - that the state was still governed by it's "ancient charter" and the laws of their state's established religion. The "degrading acknowledgements" referred to in the second paragraph of the letter, for example, were the certificates required to exempt those of other religions from paying taxes to support the Congregationalist church. By this time, Connecticut law did allow non-Congregationalists of certain denominations to have their religious taxes go to their own churches, but the process of obtaining and filing the necessary exemption certificate was made as difficult and demeaning as possible. The Baptists mention nothing whatsoever about a fear of the federal government establishing a national religion. The myth that they were writing to Jefferson for a reassurance that this couldn't happen is clearly contradicted by the third paragraph of the letter. This paragraph clearly shows that the Baptists fully understood the First Amendment and the limitations of the federal government's power. When they wrote "our constitution of government is not specific," they were referring to their state's constitution of government, not the federal Constitution. While they knew that Jefferson would be sympathetic to their situation, they also knew that he was powerless to do anything about it.

So, if the Baptists knew Jefferson had no power to help them, why did they even bother to mention the problem with their state government and its religious establishment? Jefferson's election and the ousting of the Federalist administration on the national level had given the Baptists hope that change was also possible in their state. The Baptists as well as other minority denominations in Connecticut were growing in numbers. If all of these religious dissenters joined the Republicans in Connecticut, the combination might become a political force capable of overthrowing their state's Federalist, Congregationalist government. While the religious dissenters and the Republicans had somewhat different priorities, they both had the same goals - a truly representative government and a real state constitution.

The following, dated January 1, 1802, was Jefferson's reply to the Baptist Association's letter.

Gentlemen The affectionate sentiments of esteem and approbation which you are so good as to express towards me, on behalf of the Danbury Baptist association, give me the highest satisfaction. my duties dictate a faithful and zealous pursuit of the interests of my constituents, & in proportion as they are persuaded of my fidelity to those duties, the discharge of them becomes more and more pleasing.

Believing with you that religion is a matter which lies solely between Man & his God, that he owes account to none other for his faith or his worship, that the legitimate powers of government reach actions only, & not opinions, I contemplate with sovereign reverence that act of the whole American people which declared that their legislature should "make no law respecting an establishment of religion, or prohibiting the free exercise thereof," thus building a wall of separation between Church & State. Adhering to this expression of the supreme will of the nation in behalf of the rights of conscience, I shall see with sincere satisfaction the progress of those sentiments which tend to restore to man all his natural rights, convinced he has no natural right in opposition to his social duties.

I reciprocate your kind prayers for the protection & blessing of the common father and creator of man, and tender you for yourselves & your religious association, assurances of my high respect & esteem.

One of the biggest misconceptions promoted in religious right American history books is that Jefferson's reply to the Baptists was a personal letter and/or a hastily scribbled note that he put little thought into. This is simply not true. The existing copy of the letter is actually Jefferson's first draft, not the final letter. Just the fact that he wrote a first draft proves that this was not a hastily scribbled note. Jefferson then submitted his draft to two different New Englanders in his administration, Postmaster General Gideon Granger of Connecticut and Attorney General Levi Lincoln of Massachusetts, requesting their opinions on how it would be received in their states. Obviously, Jefferson did not consider this a personal letter to the Baptist Association. He was well aware of the likelihood that such a letter would be made public, and did not want to offend any New England political allies. On the advice of Levi Lincoln, Jefferson deleted a paragraph explaining his refusal to proclaim days of thanksgiving, writing the following reason in the margin.

paragraph was omitted on the suggestion that it might give uneasiness to some of our republican friends in the eastern states where the proclamation of thanksgivings etc. by their Executives is an antient habit & is respected.

A common question about Jefferson's letter has to do with what government he was referring to. Was it the federal government or the state governments? The correct answer is both. In his letter, Jefferson described the First Amendment's establishment and free exercise clauses as an "expression of the supreme will of the nation," clearly referring to the federal government. His next sentence, however, doesn't make much sense unless he was referring to the "progress of those sentiments" in the individual states, especially given the fact that he was replying to a letter regarding the lack of religious freedom in one particular state. He couldn't have been referring to the "progress of those sentiments" in the federal government because no progress was necessary there - the First Amendment had already taken care of that. While the federal government couldn't do anything to speed up this progress in the states, Jefferson wrote that he would "see with sincere satisfaction the progress" when it was made. In Connecticut, the kind of progress Jefferson was talking about would take another 16 years.

Connecticut did eventually progress from almost complete intolerance to a degree of religious freedom on par with the other states. When the original commonwealth was formed in the 1630s, the law was simple - religions other than Congregationalism were just not allowed. In the early 1700s, it appeared that progress was being made. The law preventing Quakers from settling in Connecticut was repealed in 1702. In 1708, the General Assembly passed the Toleration Act, which allowed some privileges to certain government approved dissenting religions. These laws, however, were not were not a result of the Congregationalists becoming more tolerant, but the result of the Congregationalists' fear of royal disfavor. England's Parliament had passed an act of religious toleration in 1689, and, although the Charter of 1662 hadn't changed the laws of the state, it did include a condition that Connecticut's laws could not be in conflict with the laws of England. The General Assembly was aware that Queen Anne had received complaints of intolerance from the Quakers and, more importantly, the Connecticut Anglicans. Things started to change during the Great Awakening of the 1740s. Separatist Congregational churches began to split off from the established parish churches. This was seen as a such a tremendous threat that, in 1743, the General Assembly repealed the Toleration Act in an attempt to prevent these churches from organizing. This continued until the 1770s, when the separatists were granted a status similar to other government approved religions like the Baptists and the Quakers. This meant that worship in their churches was now considered to meet the legal requirement of attendance at a government recognized church. The sepa- ratists could no longer be fined for neglecting worship, but, like the Baptists, they had to pay taxes to the Congregational Church unless they filed an exemption certificate. Other denominations, such as the Anglicans and Episcopalians (the ones with money), had become somewhat more accepted, and had even gained a small representation in the government.

Prior to 1801, Federalist candidates in Connecticut were rarely contested. This was due, in large part, to the complete lack of secrecy in the voting process. Local elections, held at town meetings, pretty much forced the voters to vote for Federalist candidates or risk being branded troublemakers. Voters were given pieces of paper. One by one, the names of the candidates were read from a list. A voter would hand in one of their pieces of paper when the name of the candidate they wanted to vote for was called off. By always listing the Federalist candidates first, it was obvious that anyone still holding a piece of paper after all the Federalists' names had been called hadn't voted for a Federalist. In 1801, the first Republican candidates for Governor and Lieutenant Governor appeared on the ballot. The Republicans received only a small fraction of the vote, and only 33 of 200 seats in the Assembly, but the Federalists considered this enough of a threat to change the election process to further discourage Republican candidates. Up until this time, although the actual vote was far from secret, the nomination process had been done by secret ballot. In 1801 the law was changed to make nominations public as well.

The big campaign issue in the elections of the early 1800s was that Connecticut still did not have a constitution. As already mentioned, both the Republicans and the religious dissenters wanted a constitution, albeit for different reasons.The Republican priorities were separation of powers and expanded suffrage; the religious dissenters' priority was disestablishment of the Congregational church. The Republicans gained even more support when the War of 1812 ended. Funds for the war had been raised through imposing internal taxes. When the conflict was over, the U.S. Treasury had a large surplus and returned this money to the states. By giving a disproportionately large amount of this money to the Congregationalists, and little or nothing to the other denominations, the General Assembly alienated the Episcopalians. The Republicans now had the support of this large minority, which then comprised about ten percent of the population. The potential of religious dissenters combining with Jefferson's Republican party, which the Baptists had seen 16 years earlier, had became a reality. In 1817, with Oliver Wolcott running for Governor and Jonathan Ingersoll, an Episcopalian, for Lieutenant Governor, the Republicans narrowly defeated the Federalists. In the next election, the Federalists lost their majority in the Assembly. In August and September of 1818, Connecticut held its constitutional convention.

Although he was powerless to help the Connecticut Baptists in 1801, Thomas Jefferson did eventually "see with sincere satisfaction" the disestablishment of the Congregationalist Church. Upon hearing of the Republican victory in the Connecticut election of 1817, Jefferson expressed this satisfaction in a letter to John Adams.

I join you therefore in sincere congratulations that this den of the priesthood is at length broken up, and that a protestant popedom is no longer to disgrace the American history and character.