"if you make a direct contribution to an HSA (called an 'employee' contribution), you will enter an adjustment to income using the 1099 SA form you receive to document the contribution. - because, you are correct, you are contribution are after tax money."
@NCperson , I'm not sure where this came from because is not correct. There is no employment requirement for making an HSA contribution, so it makes no sense to call personal contributions "employee contributions." What TurboTax refers to as personal contributions are simply contribution deposits made directly by the individual, not through an employer.
Also, there is no adjustment to the information reported on Form 1099-SA for having made a direct contribution. As Opus 17 said, the individual receives a deduction for eligible direct personal contributions, changing the funds into pre-tax funds, resulting in all funds properly in the HSA being pre-tax funds. Unlike a traditional IRA, there is no such thing as after-tax funds in an HSA. All regular HSA distributions are treated the same on Forms 1099-SA and on the tax return, with only the amount not applied to qualified medical expenses being subject to taxation.
