We describe a new method to determine simultaneously both proliferative status and chromosome copy number within individual interphase cells. The MCF-7 human breast cancer cell line was used as a model system to characterize proliferative activity in karyotypically defined cell subpopulations. Cells were labeled with bromodeoxyuridine (BrdU) in vitro and incorporation was monitored with IU4 mouse anti-BrdU. Biotinylated, digoxigenin-labeled, or acetylamino-fluorene-conjugated repetitive sequence DNA probes were hybridized to target interphase nuclei. Three-color fluorescence labeling allowed simultaneous detection of two chromosome pairs and designation of cells undergoing DNA synthesis. This technique may also be used for simultaneous characterization of proliferative and karyotypic heterogeneity in primary human tumors.