The fluorescent vital dye rhodamine 123 (Rh-123), which preferentially accumulates in mitochondrial membranes, can be used as a probe to indicate mitochondrial and hence cellular activity. In this study, mouse bone marrow hematopoietic stem cells were subdivided into Rh-123lo, Rh-123med, and Rh-123hi populations. The Rh-123lo (resting) population was significantly enriched in cells with a higher proliferative potential compared to the Rh-123hi (activated) population. The resting population exhibited a 20-fold greater ability to differentiate into splenic colony-forming units (CFU-S) relative to the activated population, whereas the activated population contained about 4-fold more day 13 CFU-S on primary transfer relative to the resting population. The two populations produced morphologically distinct splenic colonies; however, the frequency and morphology of in vitro colonies were very similar. Only the resting population provided sufficient stem cells to transfer long-term hematopoietic repopulation to secondary recipient animals after lethal irradiation. On a single cell level, the resting and activated populations exhibited an equivalent ability to differentiate into lymphoid and myeloid progeny. These observations provide further insight into the heterogeneous nature of CFU-S and directly demonstrate that multipotent hematopoietic stem cells are heterogeneous with regard to their clonogenic capacities.