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The IRS has rolled out a Direct Pay system for making regular tax payments (balance dues from your tax return) as well as estimated payments. It is done via direct debit from your checking account. I was a little leery at first of recommending clients give bank account information to the IRS, for fear the IRS could potentially access their accounts in the event of a dispute, but the website says they do not retain account information after the payment is made. I'm not one to blindly trust the government, but I think that statement on the website would result in a whole heap of trouble for the IRS if they abused it, so I'm pretty comfortable with the system.
You can access the system HERE