On your W-2, the Box 12 code W amount includes
both the employer and employee pre-tax contributions, including
incentives. If you contributed to your HSA only through
payroll deductions, do not enter them anywhere else in TurboTax.
However, if your made after-tax contributions on your own (independent of your employer), then those contributions would be entered. You would have to enter them to calculate a deduction. Enter under the Medical section.
On your HSA summary page, you will see Tax-free employer contributions, but it means both employer and employee contributions in total. It is just how the IRS codes it (Box 12 W)
Form 1099-SA - is entered in order to calculate the deduction and complete Form 8889 properly. Form 1099-SA is issued when you have distributions from you HSA account. If you took distributions from your HSA, you need to wait for the form (must be mailed by 1/31/17). Call you the HSA custodian if you have not received this form in a timely manner.
Form 5498-SA - Just keep for your records. It is not entered in TurboTax.
Also, be certain to indicate that you were enrolled in a HDHP. This is a requirement for the participation in an HSA. If you miss entering this information, the program will calculate a contribution penalty. If you still need to know what your contributions are, look to the Form 5498-SA (may not arrive until 5/31/17) or contact your plan's custodian.
Usually, your HSA contribution is reported in box 12 of your W-2 with the code W (Company Contributions to Health Savings Account). TurboTax automatically records this amount in the 1099-SA, HSA, MSA section.
Code W reports the combined contributions from you and your employer. So if you contributed $1,500 to your HSA and your employer matched it dollar for dollar, box 12 on your W-2 would show $3,000 with a code W.
TurboTax Help FAQ: Where do I enter my HSA contribution?