Issues also arise when same-sex couples have children or other dependents, because they cannot file joint tax returns and may not both be legal parents. That complicates exemption claims and child care benefits, including education tax breaks.

PERHAPS most significantly for couples with major assets, DOMA prevents same-sex couples from taking advantage of estate tax exemptions, about $5.1 million for 2012 — but double that for couples — after indexing for inflation. If one member of a same-sex couple dies and leaves a spouse $5 million, those assets would be taxed. For heterosexual couples, there would be no tax.

That tax disparity is at the heart of the first challenge to DOMA to reach the United States Supreme Court. It was filed by Edith Windsor, who married Thea Spyer in 2007. When Ms. Spyer died in 2009, she left Ms. Windsor her share of their cottage in Southampton, N.Y., valued at $550,000 and an apartment on Fifth Avenue in Manhattan valued at $1.3 million. The result was a $600,000 federal and state estate tax bill.

“I was indignant and hurt,” Ms. Windsor said. “If her name had been Theo instead of Thea I would have owed no taxes.”

The extra costs extend even to the tax-filing process. For same-sex couples in states that recognize their marriages, couples must prepare two sets of federal returns — one that they will actually file, and another prepared as if they were married, to help prepare their state tax return.

Not having a marriage recognized for tax purposes can actually be an advantage, and the repeal of DOMA could cost some same-sex married couples some money. Just as many married couples are hit with the so-called marriage tax, many same-sex couples save money by being forced to file separately.

“I think a lot of same-sex married couples in high income ranges have no idea that once their marriage is recognized they will be paying a lot more in federal income tax because of the marriage tax penalty,” said Patricia Cain, a tax law professor at Santa Clara University, who is herself in a same-sex marriage. “I just ran the figures on a couple in the $2 million range, and in 2013 they’ll be paying $35,000 more in federal tax filing jointly.”