There could be a number of reasons this amount is different. The most common reason is normally due to contributions you make to your employer's 401k plan. Those payments are not subject to federal or state income taxes, but they are still subject to SS and Medicare taxes. So the amount you contribute to such a plan would not be included in box 1 of your W-2 form, but they would be included in boxes 3 and 5.
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Really your 401k contributions should have nothing to do with whether or not you owe tax or receive a refund. It is only the amount reported in box 1 of your W-2 that you owe tax on. And that amount has already been reduced by the amount of any 401k contributions you made.
If you owe tax this year then it can only be due to the fact that you did not have enough taxes withheld from your paychecks. It would have nothing to do with your 401k contributions. You may need to give your employer a new W-4 form to adjust your withholdings for the 2010 tax year so that more tax is taken out of your checks.
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