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Get your taxes done using TurboTax
the HSA rules
Qualified medical expenses are those incurred by the following persons.
1. You and your spouse.
2. All dependents you claim on your tax return. so it would seem you can't pay your kid's medical expenses with your HSA
3. there are additional rules but they don't apply.
Does she have an HDHP? if so and no FSA she can contribute to her own HSA (just make sure the total for both of you doesn't exceed the family maximum for the year). the family max can be split any way you want. while you can't use your HSA to pay your kid's medical expenses you can use yours to pay hers and then hers can be used to pay the kids.
have you sat down with a pro to go over your situation because married filing separately usually results in a higher tax bill due to loss of certain credits and deductions and higher tax rates which may more than offset the higher loan amount you would have to pay if filing jointly?