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My wife is starting a new job and I am trying to figure out how to file her W4 and if I need to adjust mine. For some reason I can't seem to get correct/accurate results from the IRS Withholding Calculator (for example, calculations are missing one expected paycheck).

I have computed our tax liability for this year and an estimation for how much we will owe if nothing is withheld from her paycheck.

Now I'd like to know how much will be actually withheld from her paycheck based on how she fills the W4.

Is the IRS Employer's Tax Guide (the wage bracket tables) the correct way to to this?

Assuming that her bi-weekly wage is $1538, and that the W4 will state "Married", 0 allowances and $0 additional withholding, I see that $145 should be withheld from each paycheck. Is that correct?

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Yes, there it is. Pub 15 is, in my opinion, the way to confirm your understanding. One can use the W4 worksheet, but Pub 15 tells you what result to expect.

You wrote "calculations are missing one expected paycheck." I understand this, but would not be concerned. Withholding $150 too much or too little is trivial, and you'll pay or get a refund in April, or whenever you file.

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