After receiving a 30-day letter, the taxpayer may pay the tax and then contest the assessment (unless an agreement to the contrary is executed) by filing a claim for refund or credit for all or any part of the amount paid. However, this does not apply to certain taxes determined by the Tax Court, the decision of which has become final. A claim for refund or credit is made by filing an appropriate amended return with the Internal Revenue Service Center to which the original return was sent.
When the Exempt Organizations Area Manager examines claims for refund or credit, substantially the same procedure within the Service is followed (including appeal steps) as when original exempt organizations returns are examined. The procedure for appealing rejected claims through the Court is outlined in section 601.103(c)(3) of the Statement of Procedural Rules (26 C.F.R. section 601.103(c)(3)).