You are required to report Form 8889 any HSA distributions made for the year. All money in an HSA is pre-tax, either because you make the contribution through your employer and the employer excludes the amount from box 1 of your W-2, or because you make the contribution yourself and it's turned into pre-tax by the deduction that you receive on Form 1040 line 25.
If you fail to include Form 8889 with your tax return indicating your eligibility to make the HSA contribution, the IRS will treat the contribution (reported to them on Form 5498 filed by the HSA custodian) as an excess contribution subject to a 6% excess contribution penalty each year that the excess remains in the account. A return of excess contribution is tax and penalty free except that any earnings attributable to the excess contribution must also be distributed and are subject to ordinary income tax. Unlike a return of an IRA contribution, a return of and HSA contribution is only permitted if the contribution is actually an excess contribution under the law, not because you simply changed your mind about making the contribution.
