I got the info below off of this link:
http://www.irs.gov/publications/p501/ar02.html#d0e1116.
Married Filing Separately
You can choose married filing separately as your filing status if you are married. This filing status may benefit you if you want to be responsible only for your own tax or if it results in less tax than filing a joint return.
If you and your spouse do not agree to file a joint return, you have to use this filing status unless you qualify for head of household status, discussed next.
You may be able to choose head of household filing status if you live apart from your spouse, meet certain tests, and are considered unmarried (explained later, under Head of Household). This can apply to you even if you are not divorced or legally separated. If you qualify to file as head of household, instead of as married filing separately, your tax may be lower, you may be able to claim the earned income credit and certain other credits, and your standard deduction will be higher. The head of household filing status allows you to choose the standard deduction even if your spouse chooses to itemize deductions. See Head of Household, later, for more information.
Unless you are required to file separately, you should figure your tax both ways (on a joint return and on separate returns). This way you can make sure you are using the filing status that results in the lowest combined tax. However, you will generally pay more combined tax on separate returns than you would on a joint return for the reasons listed under Special Rules , later.
How to file. If you file a separate return, you generally report only your own income, exemptions, credits, and deductions on your individual return. You can claim an exemption for your spouse if your spouse had no gross income and was not the dependent of another person. However, if your spouse had any gross income or was the dependent of someone else, you cannot claim an exemption for him or her on your separate return.
If you file as married filing separately, you can use Form 1040A or Form 1040. Select this filing status by checking the box on line 3 of either form. You also must enter your spouse's full name in the space provided and must enter your spouse's SSN or ITIN in the space provided unless your spouse does not have and is not required to have an SSN or ITIN. Use the Married filing separately column of the Tax Table or Section C of the Tax Computation Worksheet to figure your tax.
Special Rules
If you choose married filing separately as your filing status, the following special rules apply. Because of these special rules, you will usually pay more tax on a separate return than if you used another filing status that you qualify for.
Your tax rate generally will be higher than it would be on a joint return.
Your exemption amount for figuring the alternative minimum tax will be half that allowed to a joint return filer.
You cannot take the credit for child and dependent care expenses in most cases, and the amount that you can exclude from income under an employer's dependent care assistance program is limited to $2,500 (instead of $5,000 if you filed a joint return).
You cannot take the earned income credit.
You cannot take the exclusion or credit for adoption expenses in most cases.
You cannot take the education credits (the Hope credit and the lifetime learning credit), the deduction for student loan interest, or the tuition and fees deduction.
You cannot exclude any interest income from qualified U.S. savings bonds that you used for higher education expenses.
If you lived with your spouse at any time during the tax year:
You cannot claim the credit for the elderly or the disabled.
You will have to include in income more (up to 85%) of any social security or equivalent railroad retirement benefits you received, and
You cannot roll over amounts from a traditional IRA into a Roth IRA.
