Desmoid fibromatosis is a locally aggressive proliferative soft tissue lesion of controversial nature. The authors investigated the clonality of this process by molecular genetic analysis of DNA methylation pattern at a polymorphic site at the human androgen-receptor gene (HUMARA) to examine the inactivation pattern of the X chromosome. Twenty desmoid fibromatoses including primary and recurrent lesions from 11 female patients were studied. Sixteen lesions from eight patients showed nonrandom X inactivation, consistent with a clonal origin and, therefore, a true neoplastic nature. Furthermore, multiple recurrent lesions from two patients exhibited the same inactivation pattern as the corresponding primary lesions, suggesting that they were derived from the same cell clone as the primary lesion. One patient was homozygous at the HUMARA locus, and two patients had the same skewed pattern in their normal and lesional tissues. The authors also found that digestion with HpaII, but not HhaI, failed to generate a nonrandom X inactivation pattern in some of the cases, suggesting that the methylation status at the HpaII sites was altered in some lesions, and that HhaI should be used to verify results and to avoid incorrect conclusions.