I'm always confused by the working of the forms entry.
I pay into my HSA account, with pre-taxed dollars. The amount shown on my W2/Box 12c show all of my payment, but stated as "employer payments". My employer paid $1,000 into my account as a benefit. Why does it show my entire years contributions, as paid by my employer?
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I'm not sure exactly what you are asking. Any HSA contributions shown in box 12 of your W-2 with code W are called "employer contributions," even if part or all of it came out of your pay. The amount from the W-2 should be on Form 8889 line 9. If you made contributions directly to your HSA, not through payroll, that would be on Form 8889 line 2.
Are you trying to fill out Form 8889 in forms mode? That's likely to lead to errors. I suggest that you enter your HSA information using the Step-by-Step interview instead.
The TurboTax Accurate Calculations Guarantee will not apply if you make a mistake entering information in forms mode.
the portion that came from your pre-tax $'s reduced the amount on line 1 of your w-2. to prevent double-dipping, the contributions are shown as coming from your employer. since your taxable wages have been reduced by the $1,000 no HSA deduction will show up on your tax return unless you made additional contributions that did not go through your employer.
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