Abstract Our group recently developed a soft agar colony bioassay for the study of human tumor stem cells. Initial applications of this bioassay to the cytogenetic assessment of a variety of human solid tumors has been very promising. The advantages inherent to cytogenetic sampling of the clonogenic tumor cells within colonies reside in the marked quantitative and qualitative enhancement of metaphase chromosomes. Due to the large number of potentially analyzable mitotic figures in many tumor clusters following as little as 24–48 hr in culture, utilization of standard Giemsa, G-, C-, and NOR-banding techniques has been possible. We feel this technique will overcome a variety of the technical difficulties inherent to the cytogenetic study of both human solid tumors and hematopoietic malignancies.