The Smith decision caused great uproar in the religious liberty community, who felt the decision would have a dramatic negative impact on free-exercise protections in the country. This led to Congress passing a 1993 law called the Religious Freedom Restoration Act (RFRA), which restored the compelling interest test articulated in the Sherbert decision. Under RFRA, the government cannot substantially burden the free exercise of religion rights unless the government advances a compelling governmental interest in the least restrictive means. Congress passed RFRA in direct response to the Smith decision. In a sense, RFRA represented a congressional overturning of the Court’s decision. This led to another U.S. Supreme Court decision in City of Boerne v. Flores (1997), which dealt with a land-zoning dispute involving a church that wanted to expand. City officials denied the church a permit because its planned expansion would take place within the city’s historic district.

The city contended that Congress exceeded its constitutional power under Section 5 of the Fourteenth Amendment in passing RFRA and applying it to the states. The Court majority determined that RFRA swept too broadly, particularly because Congress did not have sufficient evidence of discrimination against religious freedoms in the states. In his concurring opinion, Justice John Paul Stevens added that RFRA violated the Establishment Clause by creating a governmental preference for religion. The Court’s opinion also reaffirmed the fundamental principle articulated in Marbury v. Madison that the Supreme Court has the ultimate power to determine the meaning of the Constitution:

In response to this decision, Congress passed a second law called the Religious Land Use and Institutionalized Persons Act (RLUIPA), which was similar to RFRA but not quite as broad. It applied in land use and prisoner cases but was grounded on Congress’s Commerce Clause and Spending Clause powers rather than just Congress’s powers under Section 5 of the Fourteenth Amendment. In 2005, the U.S. Supreme Court ruled in Cutter v. Wilkinson that RLUIPA did not violate the Establishment Clause but represented a permissible accommodation of prisoners’ religious liberty rights. However, other constitutional questions remain as to whether RLUIPA is constitutional. The U.S. Supreme Court likely will have to address this controversy in later cases.