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Get your taxes done using TurboTax
If you had an excess HSA contribution for 2017, you should see an entry on line 59 of your 2017 1040, and Form 5329 which shows the 6% penalty as it was computed. You would have seen a screen that said "You may want to withdraw money from your HSA." and it would have shown the amount of the over-contribution.
If when you check your return you find that you really did have an over-contribution for 2017, and you haven't withdrawn it, you can use it as your 2018 contribution. The IRS lets you roll over the contribution to 2018, and deduct it on your 2018 tax return. So you would leave the money in the account and take the deduction. You can’t apply more than you have in excess and you can’t apply more than this year’s HSA contribution limit. If the over-contribution from 2017 plus your 2018 contributions exceed your annual limit, you'll have to withdraw this year's excess by the due date of your return, including extensions. See this article for more information.
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