From Austin Cline,
Your Guide to Agnosticism / Atheism.
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Myth:
The phrase "separation of church and state" does not appear in the Constitution.

Response:
That is true, the phrase "separation of church and state" does not actually appear anywhere in the Constitution. There is a problem, however, in that some people draw incorrect conclusions from this fact. The absence of this phrase does not mean that it is an invalid concept or that it cannot be used as a legal or judicial principle.

There are any number of important legal concepts which do not appear in the Constitution with the exact phrasing people tend to use. For example, nowhere in the Constitution will you find words like "right to privacy" or even "right to a fair trial." Does this mean that no American citizen has a right to privacy or a fair trial? Does this mean that no judge should ever invoke these rights when reaching a decision?

Of course not - the absence of these specific words does not mean that there is also an absence of these ideas. The right to a fair trial, for example, is necessitated by what is in the text because what we do find simply makes no moral or legal sense otherwise. What the Sixth Amendment of the Constitution actually says is:

In all criminal prosecutions, the accused shall enjoy the right to a speedy and public trial, by an impartial jury of the State and district wherein the crime shall have been committed, which district shall have been previously ascertained by law, and to be informed of the nature and cause of the accusation; to be confronted with the witnesses against him; to have compulsory process for obtaining witnesses in his favor, and to have the Assistance of Counsel for his defence.

There is nothing there about a "fair trial," but what should be clear is that this Amendment is setting up the conditions for fair trials: public, speedy, impartial juries, information about the crimes and laws, etc. The Constitution does not specifically say that you have a right to a fair trial, but the rights created only make sense on the premise that a right to a fair trial exists. Thus, if the government found a way to fulfill all of the above obligations while also making a trial unfair, the courts would hold those actions to be unconstitutional.

Similarly, courts have found that the principle of a "religious liberty" exists behind in the First Amendment, even if those words are not actually there:

Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof...

The point of such an amendment is twofold. First, it ensures that religious beliefs - private or organized - are removed from attempted government control. This is the reason why the government cannot tell either you or your church what to believe or to teach. Second, it ensures that the government does not get involved with enforcing, mandating, or promoting particular religious doctrines. This is what happens when the government "establishes" a church - and because doing so created so many problems in Europe, the authors of the Constitution wanted to try and prevent the same from happening here.

Can anyone deny that the First Amendment guarantees the principle of religious liberty, even though those words do not appear there? Similarly, the First Amendment guarantees the principle of the separation of church and state - by implication, because separating church and state is what allows religious liberty to exist.

Related Myths about the Separation of Church and State:

The United States is a Christian Nation
Religion is necessary for good government
You have freedom of religion, not freedom from religion
This "separation of church and state" is anti-religion
The "separation of church and state" is unbiblical
This "separation of church and state" is a communist plot
The First Amendment only prohibits a national church
The First Amendment only works in one direction
The First Amendment only applies to the Federal Government
What about the "Sundays Excepted" clause?
Thomas Jefferson's letter to the Danbury Baptists is not important
An atheist, Madalyn Murray O'Hair, removed God, the Bible and prayer from public schools
God was expelled from public schools in 1962