No. Contributions to an HSA are pre-tax. They are only taxed if withdrawn and not used to pay qualified medical expenses. The remaining funds you contributed but didn't use remain in your HSA account and are available to be used in 2016 and beyond. If you withdraw funds from your HSA and don't use them to pay for qualified medical expenses they will be taxable and incur a 10% penalty. Taxpayers 65 and older can withdraw HSA funds for any reason without paying a penalty.