If they do not have an SSN or ITIN and you choose to file Married Filing Separate ,you can enter spouses name and DOB and then on the next screen you can select "xxx is a non resident alien or dual status spouse" Make sure you put a check mark in the box that says My spouse is a Non-Resident alien in the My info section. When you get to the end and try to transmit the return, ignore the e-file errors regarding your NRA spouse and select transmit your return. If that does not work you will need to print and mail your return and write NRA (Non Resident Alien) in the space for her SSN.
Even though your wife and child are Non-Resident Aliens it is still possible for you to file a joint return. The benefit to this would be if your wife does not have other income, then you would have a standard deduction of $29,200 instead of $14,600 which means your taxable income would decrease by an additional $14,600. You may also be able to claim the the$500 Other Dependent Credit.
If your spouse chooses to be treated as an US resident for tax purposes, and you want to file as Married Filing Joint and claim your child as a dependent, you can apply for an ITIN when you file your return. You would need to include their income FROM ALL SOURCES WORLDWIDE (not just what they earned in the US) on your return as well and they would be taxed on it. If you choose filing jointly, you will need to print and mail your return along with the W-7 which is an application for an ITIN and any other required documents to the address in the instructions
How should I file my taxes if my spouse is a nonresident alien?
Claiming a Non-Citizen Spouse and Children on Your Taxes
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