Money Still in Your Flexible Spending Account? Use It or Lose It

Know what’s eligible for reimbursement before developing a spending plan.

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According to Miller, the average person puts $1,500 into an FSA, so those people wouldn't be affected by the change, but about 18 percent of heavy FSA users could feel the pinch next year. Among that group are people who use FSAs in conjunction with a high-deductible health plan.

Beyond FSAs, the IRS allows taxpayers who itemize to deduct medical expenses that exceed 7.5 percent of their income. "Anything reimbursed by [an FSA] could not also be deducted," explains Thomas. However, if you had enough medical expenses that weren't reimbursed by your FSA, you might be able to deduct those expenses. In 2013, that threshold will rise to 10 percent.

If you're used to itemizing or maxing out your FSA, these changes could affect how you pay for medical expenses going forward. "Compared to prior years, someone with the same income will need to have more unreimbursed medical expenses to be able to take advantage of the deduction," says Thomas. "In theory, the cap might feed into this for someone who is used to paying $3,500 out of flex and now has to pay that $1,000 on an after tax basis and claim a deduction if available, for example. This only affects those who itemize."