Identical allelic loss in invasive and adjacent in situ ductal breast carcinoma (DCIS) on chromosome 11q13 has been previously reported, providing molecular evidence for the progression of DCIS to invasive tumor. In this study we analyzed loss of heterozygosity (LOH) on 11q13 (PYGM, INT-2) in atypical ductal hyperplasia (ADH) and various histological types of in situ carcinomas of the breast in patients without invasive cancer. Twenty-four cases of in situ carcinoma and twelve cases of ADH were studied. Tissue microdissection of normal, hyperplastic, and tumor cells from fixed, paraffin-embedded sections was performed, and DNA was extracted for polymerase chain reaction. In situ tumors included both high- and low-grade DCIS. LOH was identified in six of twenty-two (27.3%) in situ tumors and in one of eleven (9%) ADH cases. Within in situ carcinomas, LOH was identified in six of seventeen (35%) high-grade DCIS but in none of six low-grade DCIS. The present results show that LOH at 11q13 occurs in an appreciable proportion of high-grade DCIS, although the rate is substantially less than in patients with concomitant DCIS and invasive tumor. LOH was identified less frequently in low-grade in situ tumors and ADH, suggesting that a putative tumor suppressor gene(s) located on chromosome 11q13 may be involved in the transition from early preneoplastic lesions to invasive breast cancer.