It takes two accounts and two user IDs to file married filing separately--and you pay twice when you use any version of online TurboTax. With online TT you get one return per fee.
When you use Desktop TurboTax, which you install from a CD or download to your own hard drive, you can prepare and e-file multiple returns for the cost of the software. You can e-file up to 5 Federal returns—more if you mail the additional ones. If you have multiple returns to prepare for family members, Desktop is more cost effective.
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