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CUTTER V. WILKINSON (03-9877) 544 U.S. 709 (2005) 349 F.3d 257, reversed and remanded.

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A federal law prohibiting government from burdening prisoners' religious exercise did not violate the First Amendment's establishment clause. The Court held that, on its face, RLUIPA made an accommodation allowed by the First Amendment. The Court reasoned that the law was an effort to alleviate the "government-created burden" on religious exercise that prisoners faced. Nor did section three discriminate between mainstream and non-mainstream religions. The Court did point out that constitutional problems could arise if RLUIPA were enforced improperly and religious prisoners received favored treatment, or if religious exercise and security concerns were not properly balanced.
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Professor Marci A. Hamilton, TESTIMONY TO THE SENATE COMMITTEE ON THE JUDICIARY S. 1248, The Religious Liberty Protection Act of 1998

This is my testimony in opposition to the Religious Liberty Protection Act (introduced after Boerne and never passed, but the testimony re RLPA was used to defend RFRA and RLUIPA)

Professor Marci A. Hamilton, THE RELIGIOUS FREEDOM RESTORATION ACT IS UNCONSTITUTIONAL, PERIOD, 1 U. Pa. J. Const. L. 1 (1998)

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Boerne stands for the proposition that the Court's role in interpreting the Constitution was not undermined or lessened as a result of the enactment of the Fourteenth Amendment. … The law is only triggered when religious conduct is burdened by a generally applicable and neutral law.
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CITY OF BOERNE v. FLORES, 1996 U.S. S. Ct. Briefs LEXIS 761(BRIEF FOR PETITIONER)

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The Religious Freedom Restoration Act is different from any other act Congress has ever passed. Never before has Congress attempted to define for itself the core meaning of a clause of the Constitution and then to force that interpretation on the courts in every case raising the constitutional issue. This Act is unconstitutional because it goes too far.