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All of my HSA contributions were made through salary reductions last year, so they already show up on my W2 as such.

Thus, if I claim HSA contributions on Line 12 of Schedule 1, it seems like I am double-deducting HSA contributions.

In such a case, should I not claim an HSA contribution on Line 12 of Schedule 1?

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You should not claim the deduction on Schedule 1, Line 12.

There is a common misunderstanding when filling out Form 8889. On Line 2 of that form, it asks for this:

HSA contributions you made for 2019 (or those made on your behalf), including those made from January 1, 2020, through April 15, 2020, that were for 2019. Do not include employer contributions, contributions through a cafeteria plan, or rollovers (see instructions)

You might think that your payroll deduction contributions are contributions that you made, but for the purposes of this form, those are employer contributions. If all of your contributions were through payroll deduction, you need to enter 0 on this line.

Line 9 is where you enter any contributions sent in by your employer, whether they were due to payroll deduction or due to the employer adding extra money to your HSA. If you do this correctly, Line 13 of this form will be 0, and you will not have any deduction to enter into Schedule 1, Line 12.

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