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In a word, yes. Tax matters that can be pretty simple for heterosexual couples can get quite complicated for gay and lesbian couples.
However, as a result of two key rulings in 2013, tax issues just got a lot easier for many same-sex married couples.
The U.S. Supreme Court’s June 26, 2013 decision in the Windsor case made it clear that same-sex married couples living in one of the 14 U.S. jurisdictions that recognize same-sex marriage would qualify for federal benefits previously limited to opposite-sex married couples. However, the Court did not address whether the IRS (or other federal agencies) would recognize the marriages of same-sex married couples living in non-recognition states.
In August 2013, The U.S. Department of the Treasury ruled that all same-sex couples that are legally married in any U.S. state, the District of Columbia, a U.S. territory or a foreign country will be recognized as married under all federal tax provisions where marriage is a factor. This includes provisions governing:
The Treasury Department further clarified that federal recognition for tax purposes applies whether a same-sex married couple lives in a jurisdiction that recognizes same-sex marriage (such as California) or a non-recognition jurisdiction (such as Texas).
Now, legally married same-sex couples will file their 2013 federal income tax return using either the “married filing jointly” or “married filing separately” filing status. They may also choose to file an amended return as a married couple and a refund claim for tax years 2010, 2011 and 2012. And they can move about the country knowing that their federal filing status will not change.
However, the ruling made it clear that same-sex couples in a civil union or those that are currently registered as domestic partners will not qualify for federal tax benefits - couples must be legally married to qualify. However, some of these same-sex couples may find relief by claiming their partner as a dependent on their return. To learn more, see Nolo's article Claiming an Unmarried Partner as a Dependent on Your Tax Return.
On a state level, same-sex married couples will generally only receive state benefits if they live in a recognition state. Same-sex married couples living in non-recognition states will fill out their state returns as single and their federal returns as married. This can get complicated, so it's best to consult a tax professional that is knowledgeable in same-sex tax issues for help.
To learn more about tax issues, see Nolo's article Tax Issues for Same-Sex Couples.