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I'm not sure I understand what you mean by filing them "separately"?
Do you mean if you were to file two separate income tax returns?
If so, that isn't permitted. Only one return per person is allowed.
The reason it comes out better with two separate returns, is that you get double your exemptions & standard deduction.
You have to add all the figures together from the two W2s and file one Federal & one State income tax return.
It was a good idea, though. :]
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