In his opinion concurring in the judgment in Elk Grove Unified School District v. Newdow (2004) - the Pledge of Allegiance case - Justice Thomas refused to go along either with the majority’s opinion (pretending that Michael Newdow did not have standing under existing Supreme Court precedent to challenge the recitation of the Pledge of Allegiance and its “one Nation under God” phrase), or with the concurring opinions of Chief Justice William Rehnquist and Justice Sandra Day O’Connor (pretending that existing precedent in such cases as Lee v. Weisman (1992), County of Allegheny v. ACLU (1989), and Lynch v. Donnelly (1984) were somehow distinguishable because the phrase, “under God,” really has no religious meaning). “Telling either nonbelievers or believers that the words ‘under God’ have no meaning,” Justice Thomas would later remark in Van Orden v. Perry (2005), “contradicts what they know to be true.” Instead, Thomas pointed out that the 9th U.S. Circuit Court of Appeals opinion by Senior Circuit Judge Alfred Goodwin, joined by Circuit Judge Stephen Reinhardt, was a coherent application of the Supreme Court’s existing, albeit confusing, precedent. Rather than evading the problem, as the majority did, or artificially distinguishing it away, as the concurrences did, Justice Thomas took the “opportunity to begin the process of rethinking the Establishment Clause,” which is in “hopeless disarray.”

Justice Thomas has confronted the bigger issue in the establishment-clause: whether the clause properly applies to the states at all. It began with Everson v. Board of Education of Ewing (1947). Since that time little analysis exists of the Court’s decision to incorporate the establishment clause and make it applicable to the states via the 14th Amendment.

Three times in the past five years, Justice Thomas has in concurring opinions challenged Everson’s minimally reasoned holding: in the 2002 school vouchers case of Zelman v. Simmons-Harris; in the 2005 Ten Commandments case of Van Orden v. Perry; and in the 2004 Newdow case as well. In Zelman, he criticized the majority opinion of Chief Justice Rehnquist for completely “ignoring Everson” and its unrepudiated holding that “No tax in any amount, large or small, can be levied to support any religious activities or institutions, whatever they may be called, or whatever form they may adopt to teach or practice religion.” After noting that the Court simply could not “consistently leave Everson on the books and approve the Ohio vouchers” program, through which large amounts of public tax revenues would be spent on religious schools, Justice Thomas decided to confront Everson head on, finding that existing precedent based on it, if faithfully applied, would in fact render the Pledge of Allegiance unconstitutional if the erroneous precedent was not overruled.

In light of that federalism aspect of the establishment clause, the application of the clause to the states via the protection of “liberty” in the due-process clause of the 14th Amendment is particularly troubling, for as Justice Thomas noted in Newdow (and as Justice Potter Stewart had previously noted in his 1963 dissenting opinion in School District of Abington Township v. Schempp), incorporation of the establishment clause authorizes the federal government, via the federal courts, to do the very thing the clause originally prohibited it from doing.

Even more troubling to Justice Thomas than the incoherence of the incorporated establishment clause was the “handcuff[s]” that the doctrine placed on the states in dealing with matters of religion and education, preventing the States from experimenting with education.  

See also the 1952 case of Zorach v. Clauson.