The existence of mammary epithelial stem/progenitor cells has been demonstrated in MUC-1-/ESA+ subpopulations of breast epithelial cells. However, knowledge about the expression and localization in benign and malignant breast lesions is unknown. Using a double-staining immunohistochemistry method, we investigated MUC-1-/ESA+ cells in 10 normal breast tissues, 49 cases with fibrocystic disease, 40 fibroadenomas, 36 invasive ductal carcinomas and the breast cancer cell lines MCF-7 and MDA-MB-468. In normal breast tissues MUC-1-/ESA+ cells were mainly found in the suprabasal layer, but under the apical surface of the duct/alveolus. In the hyperplastic areas of fibrocystic disease, the number of this subpopulation of cells was higher than that in hypoplastic areas and in fibroadenomas. In invasive ductal carcinoma, the MMUC-1-/ESA+ cells were heterogeneously present in different carcinoma nests. In the MCF-7 cell line most cells were MUC-1-/ESA+, and in the MDA-MB-468 cell line MUC-1-/ESA+ cells and MUC-1-/ESA+ cells were almost equal. Our results show that the MUC-1-/ESA+ subpopulation increases in fibrocystic disease within the hyperplastic areas, and varies in benign and malignant breast tumours, indicating that breast carcinogenesis may develop from malignant changes of normal MUC-1-/ESA+ cells.