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I believe the OP's question was will the IRS take notice if the amount reported on the W2 12b - HSA contribution - doesn't match the amount on Form 5498 sent by the bank since they both are supposed to show the amount of contributions to the HSA for that year. Why wouldn't the employer's $1000 contribution go in box12b since that box is supposed to show funds put in by the employee via the cafeteria plan and the employer on the employee's behalf? Does the fact that is being labeled a "rebate" matter? I have a similar situation because my husband's employer did not put their contributions in box12 - just his. The money he got was for meeting certain health guidelines like being a non-smoker. How is this different than the employer putting in money for everyone unrelated to "being healthy" guidelines?