We posed this question on the IRS helpline, and we were told that interest paid on HSA accounts does count towards the annual contribution limit (and therefore, any interest paid on an HSA account would reduce the amount that could be contributed to the account). The IRS Publication on HSA accounts states that HSA accounts may earn interest, and that such interest is tax free; from that information, the IRS concluded that interest paid should be considered part of the tax free contribution. See IRS Publication 969, page 2.

You may also find this IRS FAQ helpful, as it addresses your responsibilities as custodian of HSAs. It states that a custodian is not “responsible for determining whether contributions to an HSA exceed the maximum annual contribution for a particular account beneficiary.” IRS Bulletin 2004-33, FAQ #74 (August 16, 2004).