Detection of breast cancer at an early stage is the key to successful treatment and outcome. In tumors confined to the breast at diagnosis, stage is the most important prognostic factor. If detected early, breast cancer is eminently curable. We measured loss of heterozygosity (LOH) using 9 microsatellite markers in epithelial cells obtained by ductal lavage (DL) from 59 women before breast surgery (excisional biopsies, duct resections, and mastectomies). In addition, we analyzed LOH obtained by DL in the contralateral breast of breast cancer patients. As a result, histological examination revealed 46 malignancies and 13 benign lesions. Sensitivity, specificity, and diagnostic accuracy were 100.0, 15.4, and 82.3% for LOH. LOH frequency in DL of breast cancer was significantly greater than that in DL of benign tumors. In terms of the contralateral breast of breast cancer patients, DL showed that one subject (3.4%) was malignant, and LOH frequency was similar to breast carcinoma. In conclusion, breast tissues that appear non-neoplastic pathologically often harbor genetic changes that can be important in understanding the breast environment within which the cancer develops.