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I have a copy of the check that I gave my company when I repaid that bonus, and also I have a letter of the company explaining the repayment. Should I include them in my return somehow or should I just keep them for my records?
You need to keep the records of the repayment with your other tax records. If the IRS wants to question the repayment, they will request the documentation either in a letter or if (for some reason) your return was selected for an audit.
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