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I got married in September. is it better to file jointly or separately with my spouse

 
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I got married in September. is it better to file jointly or separately with my spouse

Also, I was only married for the last 3 months of 2016 (got married at the end of September) can I still file Head of Household for 2016?

I got married in September. is it better to file jointly or separately with my spouse

NO you cannot file as head of household.  If you were married on the last day of 2016, your choices are to file as married filing jointly or married filing separately.  MFS is almost always better.  You get the $4050 exemption for each of you and the $12,600 standard deduction as a married couple (better than the $9250 as HOH, anyhow).
**Disclaimer: Every effort has been made to offer the most correct information possible. The poster disclaims any legal responsibility for the accuracy of the information that is contained in this post.**

I got married in September. is it better to file jointly or separately with my spouse

Each year you can choose to file as Married Filing Separately. However, that may not provide the benefit that you expect, and you will almost always end up paying more in tax than if you file jointly.
The Married Filing Separately filing status is very different than the Single filing status. There are a number of severe restrictions on deductions and credits, and on the amount of IRA contributions that you can deduct, especially if you live together with your spouse.
You can not take the EIC,
You can not take the credit for Child and Dependent Care, in most cases,
You can not take the Education credits/deductions, and there are many other restrictions.
 If either of you receive Social Security benefits and you live with your spouse, more of the SS benefit will be taxable, and the person receiving it will have to include the SS benefit in their gross income when determining whether they have to file. If one of you itemizes deductions, the other must also itemize even if they have nothing to itemize.

Before you decide, you should carefully read the restrictions that go with MFS in  IRS Pub. 501, at this link:
http://www.irs.gov/pub/irs-pdf/p501.pdf

You should carefully read the limits on IRA deductions in IRS Pub. 590-A at this link:
http://www.irs.gov/pub/irs-pdf/p590a.pdf

In addition, if you live in a Community Property state, there are special rules you must follow for reporting income and expense. For further information on that, see IRS Pub. 555, at this link:
http://www.irs.gov/pub/irs-pdf/p555.pdf

and/or the Turbotax FAQ at this link:
https://ttlc.intuit.com/questions/1901162-married-filing-separately-in-community-property-states
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