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Indiana does not have a reciprocal tax agreement with Illinois. If these employees are working in Illinois, they are not exempt from Illinois income tax or Illinois withholding. You must withhold Illinois tax from them just the same as you would from an Illinois resident.

If you have have employees who are working in Indiana for you, you must withhold Indiana tax. You may also withhold Indiana tax as a service for your Indiana-resident employees working in Illinois (in addition to the Illinois tax) if they request. You must register with the Indiana DOR as a withholding agent using Form BT-1. See:

http://www.in.gov/dor/3988.htm

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Q: How does an Illinois business pay the income tax for its Indiana employees?
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