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You provide the data when you complete the interview when you go to Deductions & Credits and find the section "1099-SA, HSA, MSA" under Medical (the terms may vary between versions of the product).
To complete the interview, you normally have to have the 1099-SA sent from the institution that is administering your HSA (often a bank). This will report the amount of money distributed to pay for medical expenses (usually by a debit card from that bank).
You may also receive a 5498-SA that reports the amount of contributions to the HSA, BUT because this form typically doesn't show up until after the original filing deadline, you'll want to make the entry yourself, if need be. For most employees, if the only contributions to the HSA were through employer contributions and payroll deductions, this number will appear with a code W in box 12 of the W-2. When you enter this on the W-2, the amount will carry automagically to the 8889 interview, so, in practice, all most people have to do is enter the 1099-SA information.
But be sure to complete the 8889 HSA interview! If you don't complete the 8889 correctly, the IRS will think that you spent money on non-qualified things (i.e., not medical). In fact, that is their assumption unless you tell them differently. This will cause the amount identified by Code W on the W-2 to be added back to your taxable income!
Not finishing the interview is the most common problem that people have with the 8889 and their HSAs...
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