Many tumor tissues are made up of genetically different cell populations, and the study of the causes and consequences of this heterogeneity must play a central role in cancer research. We have studied breast cancer clonal heterogeneity by cytogenetic analysis of 4123 cells from 52 successfully short-term-cultured tumorous, metastatic, and macroscopically normal breast tissue samples from 6 women with this disease. All 7 carcinomas (one woman had bilateral disease) contained 1 to 9 karyotypically related as well as unrelated clones, unevenly distributed among the tumor quadrants. Two clonal chromosome abnormalities were recurrent: interstitial 3p deletions were found in 5 carcinomas, whereas del(1)(q42) was detected in another 2 tumors. Both successfully analyzed metastatic lesions (one axillary lymph node and one metastasis in the subcutis) contained only one of several clones present in the primary tumor, thus exemplifying a reduction in overall karyotypic complexity during carcinoma spreading. In the case with the cytogenetically abnormal lymph node, another karyotypically unrelated clone was found to invade locally in the surrounding breast; also, histological evidence of carcinoma infiltration was seen in these tissue samples. In none of the other cases were clonal karyotypic changes found in macroscopically normal, extratumorous breast tissue. We conclude that a large proportion of breast carcinomas are polyclonal with cytogenetically distinct cell subpopulations expanding within separate domains of the growing tumor. Karyotypically disparate neoplastic cells may have different capacities to display malignancy-specific features (e.g., to grow invasively and set up distant metastases). It is presumed that their synergetic action is required for the full-blown carcinoma phenotype.