The Supreme Court on Wednesday grappled with whether religious schools can be excluded from government-backed scholarship programs in a case with potentially far-reaching implications for church-state relations.

The court appeared to break along familiar ideological lines, with the more conservative justices expressing concerns about whether the Montana-based dispute amounted to religious discrimination. The court’s liberal bloc, for its part, questioned if the case even presented a concrete injury for the justices to resolve.

At issue is the complex interplay between a Montana tax-credit program that stood to benefit religiously-affiliated schools, a provision of the state constitution that prohibits public aid to religious institutions and federal safeguards for religious freedom.

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The case reached the justices after the Montana Supreme Court struck down the tax-credit program, finding it violated Montana’s no-aid provision. Parents appealed over whether the Montana court decision violated the U.S. Constitution’s religion or equal protection clauses.

At the outset of oral arguments, the court's liberal justices posed tough questions to Richard Komer, a lawyer representing several Montana mothers whose children attend a Christian school and who sought scholarships under the state program.

Justice Elena Kagan Elena KaganDemocrats, advocates seethe over Florida voting rights ruling Supreme Court denies push to add Green Party candidates to Montana ballot Stakes high for Supreme Court as Trump battles for reelection MORE questioned the nature of injuries at issue given that a Montana court's decision invalidated the student aid plan for both secular and religious private schools alike.

“I guess I am having trouble seeing where the harm in this case is at this point,” Kagan said. “Because of the [state] supreme court's ruling, whether you go to a religious school or you go to a secular private school, you're in the same boat at this point.

“There is no discrimination at this point going on, is there?" Kagan asked.

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Kagan's concerns were shared by Justice Sonia Sotomayor Sonia SotomayorDemocrats, advocates seethe over Florida voting rights ruling Supreme Court refuses to halt execution of Navajo inmate amid tribe's objections Stakes high for Supreme Court as Trump battles for reelection MORE, both Obama appointees, as well as Justice Ruth Bader Ginsburg Ruth Bader GinsburgObama calls on Senate not to fill Ginsburg's vacancy until after election Planned Parenthood: 'The fate of our rights' depends on Ginsburg replacement Progressive group to spend M in ad campaign on Supreme Court vacancy MORE, a Clinton appointee.

Chief Justice John Roberts, who posed sharp questions to both sides, asked about the Montanans’ standing to sue, considering the harm was borne by schools, rather than the families.

“The injury flows through the schools, right? I mean, the money would go to the schools, not to the parents. And we don't have a school in this case,” Roberts said to an attorney for the Justice Department, who argued for the Trump administration in support of the Montana challengers.

Roberts, a George W. Bush appointee who is now dual-hatted as the presiding officer in President Trump Donald John TrumpObama calls on Senate not to fill Ginsburg's vacancy until after election Planned Parenthood: 'The fate of our rights' depends on Ginsburg replacement Progressive group to spend M in ad campaign on Supreme Court vacancy MORE’s Senate impeachment trial, has emerged as something of a swing vote on the conservative-leaning court.

Two of the court’s more conservative justices expressed concerns about the Montana constitutional provision that bars state aid to religious institutions. Critics of these so-called “no-aid clauses” say they were originally motivated by bigotry toward Catholic immigrant populations during the 19th century.

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“They're certainly rooted in grotesque religious bigotry against Catholics,” Justice Brett Kavanaugh Brett Michael KavanaughProgressive group to spend M in ad campaign on Supreme Court vacancy Senate Republicans face tough decision on replacing Ginsburg Trump reacts to Ginsburg's death: 'An amazing woman who led an amazing life' MORE asked the lawyer for the Montana government. “You agree with that?”

Justice Samuel Alito Samuel AlitoJustice Ginsburg dies weeks before election Trump's Supreme Court list reveals influence of Clarence Thomas Supreme Court deals blow to GOP in dispute over RI absentee ballots MORE later pursued a similar line of inquiry.

“Do you really want to argue that the reason why a lot of this popped up beginning, coincidentally, in the 1840s, at the time of the Irish potato famine, that had nothing to do with discrimination based on religion?” Alito asked.

Kavanaugh, a Trump appointee, and Alito, a George W. Bush appointee, are both Catholic.

Adam Unikowsky, who represented Montana, said the evidentiary record from the 1972 Montana constitutional convention where the provision was decided shows “no bigotry whatsoever.”

The Montana provision at issue makes it illegal for government entities to give “any direct or indirect appropriation or payment from any public fund or monies” to organizations “controlled in whole or in part by any church, sect, or denomination.”

This no-aid clause ran headlong into a 2015 tax credit program the Montana legislature passed to promote school choice. Under the plan, taxpayers could receive a dollar-for-dollar tax credit by donating up to $150 to organizations that awarded student scholarships.

In 2018, the Montana Supreme Court decided 5-2 that the tax credit program violated the no-aid provision, prompting the Montana parents’ appeal to the U.S. Supreme Court.

Updated at 1:38 p.m.