There could be some benefits to filing this way: Deductions or credits can now be claimed. But because of the so-called "marriage penalty"— something straight couples know all about—you may wind up paying more.
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"As a general rule, if there are two partners with a high income, they'll probably see a slightly higher tax liability," said Bob Meighan, a vice president at TurboTax. "Whereas, if one is in the low-income range and the other is the high range, they'll probably see some benefit."
Gregory Hullender and Eric Wong, who live in Seattle and work in the computer industry, were married in November. They realize they might pay a bit more this year, but they're not really worried.
"There is something exciting about this; it makes the process complete," Hullender said. "We will file one return this time and can stop attempting to track who owns what assets."
And then there are state income taxes
Same-sex marriage is not legal in most states. If a gay couple got married in one state but live in or move to another that does not recognize their marriage, each spouse may have to file a "single" state income tax return.
"It's a patchwork of rules out there right now," Meighan said. "If you're in a state that recognizes same-sex marriage, that's good news. If not, are they going to honor the federal requirement for joint filing or are they going to require the partners to file separately?"
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Each state gets to make up its own rules for filing state income taxes, and in some cases, those rules are still in flux. Some states have created new forms for same-sex couples to use if they file a joint federal return.
"I see a tremendous amount of confusion," said Janis Cowhey McDonagh, co-leader of the LGBT Practice group at the accounting firm Marcum LLP. "People don't understand what their state requires, even if it recognizes their marriage. And things keep changing, so there's a lot to keep up with."
For example, a federal judge recently overturned Utah's ban on same-sex marriages. A later ruling blocked that decision until it could be appealed by the state. Between those two rulings, more than 1,000 same-sex couples married in Utah.
Last week, Utah's governor sent out a memo saying, "State recognition of same-sex marital status is ON HOLD until further notice."
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But U.S. Attorney General Eric Holder said the federal government will recognize those marriages, so those Utah couples married by Dec. 31 will file as married on their federal return.
Taking a look at past returns
Couples who have been married in a state that recognized gay marriages before 2013 should look at their prior returns to see if they should refile them.
"You're not obligated to amend prior returns, but some couples might find that it's beneficial. You can do that for three years," explained Annette Nellen, director of the graduate tax program at San Jose State University. "For example, if two years ago, one spouse had a big capital gain and the other had a big capital loss, they can amend that year's returns—to change to a joint return—and use the loss against the gain."
—By CNBC contributor Herb Weisbaum. Follow him on Facebook and Twitter @TheConsumerman or visit The ConsumerMan website.