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You do not have to accept any audit report; you can appeal it by sending a protest letter to the IRS within 30 days after receiving the audit report. If you request an appeals consideration, you will be granted a meeting with an appeals officer who is not part of the IRS division that performed your audit.
If your appeal fails, you can then file a petition in tax court. This is a fairly inexpensive and simple process, if the audit bill is for less than $50,000. If it's for more, you will most likely need the help of a tax attorney.
Generally, it pays to contest an audit report by appealing and going to court. About half the people who challenge their audit report are successful in partially lowering their tax bill.