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OBJECTIVE Because almost all malignancies represent monoclonal proliferations, we have studied the clonal status of peripheral papillomas (peri-PM), ductal carcinomas in situ (DCIS), and normal breast tissues to explore a reliable way to distinguish benign and malignant (or pre-malignant)cases previously diagnosed morphologically.METHODS Twenty-six cases of peri-PM, 25 cases of peri-PM with atypical ductal hyperplasia (ADH), 27 cases of DCIS, 16 cases of developed canceration and 20 specimens of normal tissue were examined in the study. The clonal status of these tissues was studied using an assay based on inactivation mosaicism of the lenth-polymorphic X-chromosomes at the androgen receptor (AR) locus.RESULTS Loss of polymorphism at the AR locus was found in all DCIS cases and 10 cases (10/25, 40.0%) of peri-PM with ADH, indicating the monoclonality of the tumors. Twenty-four out of 26 (92.3%) cases with periPM and 19 specimens of normal tissue were shown to be polyclonal. In 16 cases of developed canceration, identical X chromosome inactivation (monoclonal alterations) was observed from both the peri-PM with ADH part, and the DCIS part in each case.CONCLUSION These results contribute to the understanding of the genetic changes of peri-PM, and confirm the peri-PM with ADH as a precancerous lesion of the breast. Clonal analysis might be a useful modality to screen high-risk cases from precancerous lesions or to distinguish between benign hyperplasia and early carcinoma.