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I am in US on a F1 visa. While working on OPT, F1 visa holder does not have to pay social security and medicare taxes.

However my spouse in on H1B visa. Since we file jointly we pay social security and medicare taxes for both. Today my HR told me that I do not need to pay these taxes and that they are going to update my withholding accordingly.

If HR is right, I will need to file an amendment to my tax return. However I think they are incorrect and that I should be paying these taxes. Who is correct?

BTW I have been in US for more than 5 years and therefore file as a resident instead of non-resident.

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Only nonresident alien F1 are exempt from FICA taxes (Social Security tax and Medicare tax); resident alien F1 are still subject to FICA taxes (except students on in-school employment). Since according to you you are a resident alien because you have been here more than 5 calendar years, you are subject to FICA taxes, regardless of whether you file jointly with your spouse or not.

You should inform your employer that you are not exempt from FICA because you are a resident alien, and they should withhold FICA taxes from you. However, withholding it is the employer's responsibility, and it is they who owe the taxes to the government, not you. If they refuse to withhold it, there is nothing you can do, and nothing you need to worry about.

The tax return is about income taxes. FICA taxes are generally not reported on the tax return, and do not affect your income taxes. There is nothing you need to "amend" on your tax return.

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