Multi-color fluorescence in situ hybridization (FISH) can determine the changes in the copy numbers of several chromosomes simultaneously and can therefore be used to identify aneusomic patterns in individual cells. Aneusomic patterns may be useful for determining the malignant nature of rare epithelial cells in the blood of cancer patients. Touch preparations from 74 primary breast tumors were evaluated for aneusomy of chromosomes 1, 8 and 17 by tri-color-FISH. In the first part of the analysis, percentages of aneusomy for individual chromosomes and their combinations were determined. In the second part of the analysis, aneusomic patterns for these three chromosomes were analyzed in individual tumor cells and compared to aneusomic patterns observed in leukocytes and in individual cells from benign and normal breast tissue to determine aneusomic patterns indicative of malignancy. Ninety-two percentage of the primary breast carcinomas showed aneusomy for one or more enumerator probes. Comparison with benign breast tissue identified six aneusomic patterns in individual carcinoma cells indicative for malignancy by statistical analysis and not observed in leukocytes. Hence, certain patterns of aneusomy in individual cells involving chromosomes 1, 8 and 17 are indicative of malignancy in individual breast tumor cells and may be useful for determining malignancy of rare epithelial cells in the blood of breast cancer patients.