Cytogenetic analysis of tumor cells from a human malignant melanoma was performed on both the primary tumor colony-forming cells and a cell line (HA-A) established subsequently from the clonogenic population. Chromosome-banding analysis demonstrated identical karyotypic alterations in both the tumor colony-forming cells and the HA-A cell line, documenting their origin from a common precursor. The most distinctive chromosome alterations shared between tumor colony-forming cells and the HA-A cell line were double-minute bodies (DMs) and a homogeneously staining region (HSR) on chromosome 7 at band p22. This represents the first observation of DMs or HSRs in cells from a human malignant melanoma. The frequency of HSR-bearing cells observed in the original tumor was less than 1%, while DM-containing cells were present in greater than 90% of all cells examined. In contrast, serial chromosome harvests at early passage of the HA-A cell line revealed positive selection for HSR-bearing cells with concomitant loss of DM-containing cells after increasing time in vitro. Following the ninth serial passage in vitro, HSRs were observed in 100% of cells with DMs no longer observed in the HA-A cell line. The finding of an HSR-bearing marker in the original tumor sample supports the view that HSRs are not an artifact of in vitro monolayer growth. However, our results demonstrate that the frequency of HSR-bearing cells within established cell lines may reflect in vitro selection and therefore not accurately reflect the frequency of this population in vivo.