I just filed my fed and state taxes and paid with deduction from bank account. I owe a penalty for having too much money in my IRA, how do I pay that?

[ThomasM · Accepted solution]

Additional taxes on excess contributions or excess accumulation are calculated on Form 5329 and are already figured into the bottom line of your tax return.  So when you pay what's owed on the return, those taxes are included.  You won't pay them separately.

You'll see the additional tax on line 59 of the 1040, with the caption Additional tax on IRAs, other qualified retirement plans, etc.