The U.S. Supreme Court case Cutter v. Wilkinson, 2004, revolved around the issue of religious rights for inmates in state prisons. The plaintiffs were a group of Ohio prisoners who followed non-mainstream religions and sued under the Religious Land Use and Institutionalized Persons Act (RLUIPA), which prohibits governments from imposing burdens on prisoners' religious exercises unless they are necessary to further a compelling government interest. They claimed that prison officials violated their First Amendment rights by not accommodating their religious practices such as providing ceremonial items and special diets. The defendants argued that RLUIPA was unconstitutional because it advanced religion in violation of the Establishment Clause. The Supreme Court unanimously ruled in favor of the plaintiffs, holding that RLUIPA made an accommodation allowed by the First Amendment rather than breaching separation between church and state principles enshrined within it; thus, it did not violate the Establishment Clause.

In the dissenting opinion for Cutter v. Wilkinson, Justice Thomas argued that the Religious Land Use and Institutionalized Persons Act (RLUIPA) was unconstitutional because it violated the Establishment Clause of the First Amendment. He believed that RLUIPA gave preferential treatment to religious rights over other constitutionally protected interests, thus violating principles of neutrality towards religion. Furthermore, he expressed concern about how courts would determine what constitutes a "substantial burden" on an inmate's exercise of religion under RLUIPA. This could potentially lead to arbitrary decisions based on judges' personal interpretations rather than clear legal standards. Overall, while acknowledging Congress’s good intentions in protecting religious freedom for institutionalized persons, Justice Thomas felt that RLUIPA went too far and infringed upon constitutional boundaries between church and state.