As of September 16, 2013, through Revenue Ruling 2013-17, the Internal Revenue Service will recognize the marital status of legally married persons, including persons married to others of the same sex, for the purposes of filing federal income tax returns. The full text of Rev. Rul. 2013-17 can be found here.
Currently, thirteen states recognize same-sex marriage. Rev. Rul. 2013-17 will require same-sex spouses who were legally married in any jurisdiction to select a filing status of married filing jointly or married filing separately beginning in 2013, regardless of whether the state in which the person resides recognizes same-sex marriage. This ruling also covers income and gift and estate taxes. It applies anywhere marriage is a factor, including but not limited to filing status, claiming personal and dependency exemptions, taking the standard deduction, employee benefits, contributing to an IRA, claiming the earned income tax credit or child tax credit, and employees who purchased same-sex spouse health insurance coverage from their employers on an after-tax basis may treat the amounts as pre-tax and excludable from income.
Individuals who were in same-sex marriages in the past may, but are not required to, file amended returns for past years during the marriage. Generally, the statute for filing a refund claim is three years from the date of filing or two years from the date upon which the tax was paid, whichever is later. Therefore, amended returns seeking refunds should be honored for 2010, 2011, and 2012. Same-sex spouses that have not yet filed their 2012 federal income tax return will have the option of filing as married or not married.
While the ruling recognizes all legal marriages, it does not apply to civil unions, domestic partnerships, or other formalized relationships that are not marriage.