Focal nodular hyperplasia (FNH) of the liver is a benign tumor commonly considered as a reactive disorder related to a pre-existing vascular malformation. However, the pathogenesis of this lesion has been recently discussed. To determine whether FNH is a polyclonal or a clonal lesion, we investigated the inactivation pattern of the X chromosome, using molecular genetic analysis of the DNA methylation pattern at a polymorphic site on the human androgen receptor gene (HUMARA). Fifteen FNH were studied, and results were compared with those obtained from 7 hepatic adenomas (HA) and 2 hepatocellular carcinomas (HCC). DNA was extracted from both lesional and nonlesional livers, fixed, and paraffin-embedded. To assess the methylation pattern, we used a quantitative fluorescent polymerase chain reaction (PCR) procedure that allows for the accurate measurement of the peak intensities of each allele. Three patients were noninformative because they were homozygous at the HUMARA locus. According to the threshold for monoclonality established by a titration curve, all FNH showed a random pattern of X-chromosome inactivation consistent with a polyclonal lesion. In contrast, all but 1 hepatic adenoma and all hepatocellular carcinomas were clonal, as shown by the nonrandom pattern of X-chromosome inactivation observed in these cases. In conclusion, these results suggest that FNH should be considered as a reactive disorder rather than as a tumoral proliferation. Discordant results recently observed in the literature could be at least in part explained by methodological differences in the PCR procedure.