As noted above, there are so many reasons why Box 1 might be less than Box 3, including Health Insurance or education assistance, or an FSA plan for something like child care benefits. Box 12 information will often give clues about the difference between the 2 boxes, or sometimes the difference is in Box 10. Paystubs often are valuable in listing all the pretax deductions too. If you really can't find any information on your pay stub or W-2, you would have to ask your employer. It's always worth looking over your W-2 and pay stubs carefully because payroll people sometimes do make mistakes, so it's good that you are so attentive.
