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If you have high deductible plan and funded your own HSA (not through your employer or withholding from your paychecks), you will deduct it on line 25 of 1040 to make it pre-tax. You will also have to include form 8889 with your return.
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You have to start with 8889. You start with the line 1 by choosing your plan and put your contribution on line 2. You follow the lines down to the line 13. Your contribution will be carried over from line 13 to line 25 on 1040.