Employee contributions to a 401(k) are reported in Box 12 of Form W-2 with Code D. Those contributions/elective deferrals have to be run through payroll. While the amount withheld and contributed to the 401(k) is not subject to federal and state income tax it is subject to Social Security and Medicare and reported in boxes 3 and 5 of the W-2 as applicable. Being a high wage earner does not make 401(k) contributions taxable, but if the plan is "Top Heavy" then highly compensated employees may be limited to the amount they can contribute. Excess contributions are subject to an excise tax each year until removed. For additional information see the following IRS web page: 401(k) Plans
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