For many taxpayers,
contributions to their HSA are reported on their W-2 in box 12 with a code of a code of "W". This is for employer contributions as well as employee contributions that are made through a payroll deduction process using a salary reduction agreement.
There is also form
5498-SA which lists contributions to your HSA, but this form often comes out too late to file your return on time. For the majority of taxpayers whose contributions were reported on the W-2, it is not necessary to wait for the 5498-SA.
Note that independent contributions can also be reported in TurboTax in the HSA interview.
Form 1099-SA is a report from the HSA plan administrator to you on how much was "distributed" from the HSA, i.e., used to pay for qualified medical expenses (usually through a debit card).
Form 8889 is completed by TurboTax based on the W-2 and the answers in the HSA interview. This form documents the contributions and distributions and reports on any penalties or taxable events.
If you have any contributions to or distributions from your HSA in a year, then the IRS requires you to file form 8889, which is part of TurboTax Deluxe and higher versions.
The HSA interview can be entered in most versions of TurboTax by going to Federal Taxes->Deductions & Credits->Medical->HSA, MSA Contributions. Once you start the interview, be sure to complete it.
