A taxpayer may petition the Tax Court for redetermination of their deficiency within 90 days of the mailing of a notice of deficiency according to Code Section 6213(a). If the 90 day deficiency notice was used by the Appeals Office, it is possible to arrange for pretrial settlement with the Regional Counsel of the IRS. This can be accomplished even after the case has been docketed in the Tax Court.
Small Tax Cases
Taxpayers filing a petition with the Tax Court may have their case handled under less formal rules applicable to small tax cases if the amount of the deficiency or claimed overpayment is equal to or less than $50,000. However, small tax cases do not have the option to appeal once a decision is made and are treated as precedents for any other cases.
90 Day Rule
In the event a taxpayer does not file a petition with the Tax Court within 90 days, the opportunity to appeal to the Tax Court is lost. This is a very strict rule and there is no way around it unless you can prove that you were never given a 90 day letter. In the event you are unable to proceed to Tax Court, you may be able to have your case heard in another court system.
Paying & Filing a Suit
Another option allows the taxpayer to pay the deficiency and file a claim for refund by filing Form 1040X (Amended U.S. Individual Income Tax Return) and mailing it to the IRS Center where the taxpayer filed the original return. A claim of refund must be filed within three years from the date the return was filed or within two years from the date the tax was paid, whichever is later. If the return was filed before the due date, the three year period starts to run from the date the return was due.
A suit to recover a refund may not be started until six months from the date the taxpayer filed the claim for refund, unless a decision on the claim for refund was made before then. A suit for refund must be started before the end of two years from the date of mailing of a notice to the taxpayer disallowing part or the entire claim.