A 25-year-old female with familial adenomatous polyposis (FAP) presented with an abdominal tumor just below the scar due to a colectomy performed 15 months previously. This tumor (tumor A) measured 7 cm in diameter, was diagnosed as a desmoid tumor of the abdominal wall, and was excised. Despite the subsequent administration of sulindac (300 mg daily for 1 year), a desmoid tumor recurred at the same site. Excision was performed again when the tumor was 8 cm in diameter, and examination revealed it to consist of a large tumor (B) and a small tumor (C) that bulged out from tumor B. Germ-line APC analysis showed a C deletion at codon 1460 resulting in a stop codon. Two somatic mutations were observed in tumor A: a TCAA deletion at codon 1068 and a deletion of a codon at bp 1192-2097. In tumor B, a somatic mutation was found at codon 1041 changing CAA to TAA. We could not detect any somatic mutations in tumor C. We conclude that somatic mutation analysis of the APC gene can be used to identify whether a recurrent desmoid tumor in a patient with FAP is a new primary tumor or a recurrence from microscopic remnants of the original tumor.