The flag flies in the wind in front of the Supreme Court in Washington, Monday, June 22, 2015. (AP Photo/Susan Walsh)

The Supreme Court on Friday ruled 5-4 that the Constitution requires that same-sex couples be allowed to marry no matter where they live and that states may no longer reserve the right only for heterosexual couples.

The case has raised questions over how legalizing gay marriage would affect religious institutions.

During oral arguments in March, Justice Samuel Alito compared the case to that of Bob Jones University, a fundamentalist Christian university in South Carolina. The Supreme Court ruled in 1983 the school was not entitled to a tax-exempt status if it barred interracial marriage.

Solicitor General Donald B. Verrilli Jr., arguing for the same-sex couples on behalf of the Obama administration, said,”You know, ­­I don’t think I can answer that question without knowing more specifics, but it’s certainly going to be an issue. I don’t deny that. I don’t deny that, Justice Alito.  It is –it is going to be an issue.”

[Could religious institutions lose tax-exempt status over Supreme Court’s gay marriage case?]

Friday’s ruling will raise questions again on that issue.

Here’s a key section on religious views from the majority ruling:

“Many who deem same-sex marriage to be wrong reach that conclusion based on decent and honorable religious or philosophical premises, and neither they nor their beliefs are disparaged here. But when that sincere, personal opposition becomes enacted law and public policy, the necessary consequence is to put the imprimatur of the State itself on an exclusion that soon demeans or stigmatizes those whose own liberty is then denied. Under the Constitution, same-sex couples seek in marriage the same legal treatment as opposite-sex couples, and it would disparage their choices and diminish their personhood to deny them this right.”

Here’s another key section on religion from the majority opinion:

“Finally, it must be emphasized that religions, and those who adhere to religious doctrines, may continue to advocate with utmost, sincere conviction that, by divine precepts, same-sex marriage should not be condoned. The First Amendment ensures that religious organizations and persons are given proper protection as they seek to teach the principles that are so fulfilling and so central to their lives and faiths, and to their own deep aspirations to continue the family structure they have long revered.”

In his dissent, Chief Justice John Roberts Jr. discussed religious liberty concerns.  “Today’s decision, for example, creates serious questions about religious liberty,” Roberts wrote. “Many good and decent people oppose same-sex marriage as a tenet of faith, and their freedom to exercise religion is—unlike the right imagined by the majority— actually spelled out in the Constitution.”

“Respect for sincere religious conviction has led voters and legislators in every State that has adopted same-sex marriage democratically to include accommodations for 28 OBERGEFELL v. HODGES ROBERTS, C. J., dissenting religious practice. The majority’s decision imposing same-sex marriage cannot, of course, create any such accommodations. The majority graciously suggests that religious believers may continue to “advocate” and “teach” their views of marriage. Ante, at 27. The First Amendment guarantees, however, the freedom to “exercise” religion. Ominously, that is not a word the majority uses.”

Roberts noted that the question of tax-exempt status of religious institutions could become an issue.

“Hard questions arise when people of faith exercise religion in ways that may be seen to conflict with the new right to same-sex marriage—when, for example, a religious college provides married student housing only to opposite-sex married couples, or a religious adoption agency declines to place children with same-sex married couples. Indeed, the Solicitor General candidly acknowledged that the tax exemptions of some religious institutions would be in question if they opposed same-sex marriage. See Tr. of Oral Arg. on Question 1, at 36–38. There is little doubt that these and similar questions will soon be before this Court. Unfortunately, people of faith can take no comfort in the treatment they receive from the majority today.”

Justice Clarence Thomas issued the following on religious liberty in his dissent:

“Aside from undermining the political processes that protect our liberty, the majority’s decision threatens the religious liberty our Nation has long sought to protect. Numerous amici—even some not supporting the States—have cautioned the Court that its decision here will “have unavoidable and wide-ranging implications for religious liberty.” Brief for General Conference of Seventh-Day Adventists et al. as Amici Curiae 5. In our society, marriage is not simply a governmental institution; it is a religious institution as well. Id., at 7. Today’s decision might change the former, but it cannot change the latter. It appears all but inevitable that the two will come into conflict, particularly as individuals and churches are confronted with demands to participate in and endorse civil marriages between same-sex couples.”

He also wrote the following on religious liberty.

“Although our Constitution provides some protection against such governmental restrictions on religious practices, the People have long elected to afford broader protections than this Court’s constitutional precedents mandate. Had the majority allowed the definition of marriage to be left to the political process—as the Constitution requires—the People could have considered the religious liberty implications of deviating from the traditional definition as part of their deliberative process. Instead, the majority’s decision short-circuits that process, with potentially ruinous consequences for religious liberty.”

Read the court’s full opinion here.

Want more religion coverage? Follow Acts of Faith on Twitter or sign up for our newsletter.

10 key excerpts from Pope Francis’s encyclical on the environment

Washington National Cathedral dean: It’s time to remove stained-glass windows with Confederate flags