Opposing the church was the ACLU, which had argued that to make the church eligible for state benefits would be an unconstitutional violation of the establishment clause.
Missouri's denial of the church, however, "goes too far" under precedents of Supreme Court decisions, Chief Justice Roberts wrote, and "violates the Free Exercise Clause."
The Missouri law was passed during a time when many other states were passing laws barring public funding of sectarian schools, widely viewed at the time to mean Catholic schools and other religious schools that were not part of the public school system. The laws were modeled after the federal Blaine Amendment, proposed in the 1870s and named after Maine Congressman James Blaine. His amendment was proposed, but never passed by Congress.
In oral arguments in the case, justices also discussed the broader constitutionality of religious groups having access to other public benefits, including a Jewish synagogue requesting a security detail.
Catholic leaders applauded Monday's ruling.
"The Supreme Court is signaling in this decision that the government must stop its growing hostility towards religion and religious institutions, and that antiquated and anti-Catholic Blaine Amendments should not be used as a weapon to discriminate against people of faith," Maureen Ferguson, senior policy advisor with The Catholic Association, stated.
"For over a century, Blaine Amendments have enshrined into law discrimination against faith-based charities and schools that form an essential part of American society," Ashley McGuire, senior fellow with The Catholic Association, stated. "In this case, a state Blaine Amendment was used to justify blacklisting a Christian elementary school from a playground safety program solely on religious grounds."
"Blaine Amendments are anti-Catholic in their origin, and getting rid of them is more than a century overdue," she added. "Today's decision demands a more fair and inclusive approach to government programs meant to serve all people."
The decision "will have an effect" in the future, David Cortman, senior counsel with Alliance Defending Freedom, who argued the case for the church before the Court in April, said. "Whenever religious people, organizations, see themselves being discriminated against, this case will be the controlling precedent," he added.
Members of Congress also weighed in on the decision. House Speaker Paul Ryan (R-Wisc.) called it "an important ruling for religious liberty with profound significance for America's civil society."
Sen. James Lankford (R-Okla.), co-chair of the Congressional Prayer Caucus and who filed an amicus brief with colleagues on behalf of Trinity Lutheran in the case, stated that "today's decision affirms the First Amendment right to the free exercise of religion-to have more than just a belief but to live out your faith without discrimination from the government."
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The case was ultimately between the church and the state's natural resources department. Missouri's attorney general recused himself in the case.
Missouri's governor Eric Greitens (R) had already announced that in the future, religious institutions could be eligible for benefit programs of the natural resources department. However, the Court stated on Monday that "that announcement does not moot this case."
Justice Sonia Sotomayor, in her dissent, stated that "this case is about nothing less" than the relationship "between church and state."
"The Court today profoundly changes that relationship by holding, for the first time, that the Constitution requires the government to provide public funds directly to a church," she added. "Its decision slights both our precedents and our history, and its reasoning weakens this country's longstanding commitment to a separation of church and state beneficial to both."
In the majority opinion, Chief Justice Roberts acknowledged that "it is true the Department has not criminalized the way Trinity Lutheran worships or told the Church that it cannot subscribe to a certain view of the Gospel."
"But, as the Department itself acknowledges, the Free Exercise Clause protects against 'indirect coercion or penalties on the free exercise of religion, not just outright prohibitions.'" And a church being denied participation in public benefits because of its religious character can be such an "indirect coercion" on the free exercise of religion, he continued.