If you have filed an amended return or refund claim for a refund of taxes you have paid, and the IRS has denied your claim for refund, the only courts with jurisdiction to hear your case are United States district courts or the Federal Court of Claims (located in Washington, D.C.). If the taxes you are contesting have been paid in full, you have filed a refund claim, and you have been sent a “notice of disallowance” of that claim by the IRS, you have two years from the first notice of disallowance you have received (subsequent or reconsidered notices don’t extend the time) to file an action for refund in district court or the Court of Claims.
On the other hand, if you have been audited and the audit has been finalized – meaning you have been issued a “Notice of Deficiency” – and you haven’t fully paid the taxes the IRS says you owe, you may file a petition to litigate the matter in United States Tax Court. However, you must do so within 90 days of the date of the Notice of Deficiency.
If you are thinking of fighting the IRS in court, it is always a good idea to consult a tax professional to make sure you know, and take full advantage of, your rights at the earliest time possible.