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You will probably need to file with both states. WI, as your resident state, is entitled to tax both paychecks. Since IL & WI have a reciprocity agreement, you will not owe tax to IL; however, since your wife's W-2 apparently has IL tax withheld, you will have to file an IL tax return to get a refund.
Your wife needs to file a Form IL-W-5-NR with her employer to stop her IL withholding as a WI resident. The form is available at http://www.revenue.state.il.us/TaxForms/Withholding/IL-W-5-NR.pdf .
Your wife needs to file a Form IL-W-5-NR with her employer to stop her IL withholding as a WI resident. The form is available at http://www.revenue.state.il.us/TaxForms/Withholding/IL-W-5-NR.pdf .
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