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@470pitt wrote:

Yes box 3 is lower but only by the amount of the 401K D amount

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Box 1 should be lower than Box 3/5 by the 401K (D) and HSA (W) amounts, or the employer needs to issue a corrected W2.  Im wrong, but you may see the difference in the state wages, some states dont conform to the tax deduction.

Anything that gets contributed through payroll should be included on the W2, you dont enter that again on the 8889.