In this study, we compared genetic instability in 70 breast carcinomas analyzed by two different methods, cytogenetics and flow cytometry. This comparison showed that each method has its strengths and weaknesses. Flow cytometry detected aneuploidy in 60% of cases, but missed most of the cytogenetically near-diploid clones and clones with simple chromosomal changes. Cytogenetics revealed chromosomal abnormalities in 50% of the samples. Simple chromosomal changes and multiploidy were readily detected by this method, but some of the clones with a high DNA index by flow cytometry were missed. The two methods gave corresponding results in the majority of cases (54%). In 17 cases, both methods detected matching abnormal clones (r = 0.93) but the DNA index was higher than predicted by the chromosome numbers. Most of the discrepancies might be explained by tumor heterogeneity and insufficient numbers of cells available for cytogenetic analyses. In seven cases, single-cell abnormalities were found that corresponded to a flow cytometry peak. Multiclonality was present in 25% of aneuploid tumors. No association was found between metaphases in cytogenetic preparations and increased S-phase fraction of the tumors, but aneuploid tumors had a significantly higher proliferation rate. Pooling data from both methods demonstrated that the majority of our samples were aneuploid (74%).