By Bob Van Voris – Sep 27, 2012 12:00 AM ET

The Defense of Marriage Act, which bars the federal government from recognizing same-sex unions, faces a challenge from a lesbian spouse whose lawyer is scheduled to make arguments to a U.S. appeals court.

A three-judge panel in New York today is set to consider arguments from Edith Windsor, who sued over a $363,000 federal tax bill she received after the 2009 death of her spouse, Thea Spyer. Their marriage, which was performed in Canada, was recognized under the laws of New York, where the couple lived. Windsor would have been exempt from the taxes if she had been married to a man. A federal judge in Manhattan sided with Windsor in June, finding the Defense of Marriage Act unconstitutional.

The case follows a May decision by the U.S. Court of Appeals in Boston that the law, which defines marriage as only between a man and a woman, is unconstitutional. That is the only ruling by a U.S. appeals court finding DOMA unconstitutional.

“The main issues in these cases revolve around equal protection, the idea that this federal law treats similarly situated people differently,” said Jonathan Entin, who teaches constitutional law at Case Western Reserve University law school in Cleveland.

Entin said he expects the final decision on whether DOMA is constitutional will rest with the U.S. Supreme Court.

James Esseks, director of the American Civil Liberties Union’s Lesbian Gay Bisexual and Transgender Project, said justifications for DOMA by its supporters amount to little more than “discomfort with gay people” and with same-sex marriage. The ACLU is helping Windsor challenge the law.

Bill Clinton

DOMA, which was signed into law by President Bill Clinton in 1996, affects more than 1,000 federal laws that refer to marriage, according to the opinion by the Boston-based appeals court. The law may affect more than 100,000 couples, the judges said.

“The denial of federal benefits to same-sex couples lawfully married does burden the choice of states like Massachusetts to regulate the rules and incidents of marriage,” the court said in its ruling.

In February, U.S. Attorney General Eric Holder told Congress that the Obama administration would no longer defend DOMA. The case for upholding the law is being argued in the Windsor case by the Bipartisan Legal Advisory Group of the U.S. House of Representatives.

‘Relatively Novel’

Gregory Katsas, who defended DOMA as assistant attorney general for the Justice Department’s Civil Division in the administration of President George W. Bush, said one of the strongest arguments DOMA supporters point to is the long history of defining marriage as a union between a man and a woman.

“Same-sex marriage is something that’s relatively novel and not that widely accepted,” said Katsas, now a partner with the Jones Day law firm in Washington. He said it’s a “hard sell” for the opponents to argue that Congress had no rational basis for restricting marriage to heterosexual couples.

Windsor, who worked for International Business Machines Inc., and Spyer, a clinical psychologist, met in 1963 and became engaged in 1967, according to the complaint filed in the case. They married Toronto in 2007. New York, which didn’t allow gays and lesbians to marry at the time, recognized same-sex unions that were performed in jurisdictions where they were legal. Last year New York Governor Andrew Cuomo signed a law legalizing gay marriage in the state.

The case is Windsor v. U.S., 12-2435, U.S. Court of Appeals for the Second Circuit (Manhattan).

To contact the reporter on this story: Bob Van Voris in New York at rvanvoris@bloomberg.net

To contact the editor responsible for this story: Michael Hytha at mhytha@bloomberg.net