A major obstacle to stem cell gene therapy is the extremely low efficiency of stem cell transduction. In vivo selection is a strategy for enriching a minor population of genetically modified bone marrow cells through the introduction of a drug resistance gene, followed by subsequent administration of the corresponding cytotoxic drug in vivo. Achieving persistent effects from in vivo selection is expected to require selection at the level of stem cells or, minimally, selection at the level of progenitors. Major limitations to in vivo selection are the nonhematologic toxicities of the cytotoxic drugs used and the resistance of stem cells and progenitors to killing by most cytotoxic agents. Experiments were performed in mice to evaluate whether the drugs used for selection in combination with multiple drug resistance gene 1 (MDR1) could have an enhanced effect on clonogenic progenitors if preceded by administration of the cytokine, stem cell factor (SCF). Single doses of taxol, navelbine, or vinblastine produced 10-fold reductions in the total number of mononuclear cells per femur, indicating a significant depletion of nonclonogenic precursor cells. However, for each of these agents, clonogenic progenitors, assayed as colony-forming unit cells and day-12 spleen colony-forming units, were relatively spared. Administration of SCF before taxol, navelbine, or vinblastine completely abrogated the progenitor-sparing phenomenon, because clonogenic progenitors were depleted as effectively as nonclonogenic precursor cells. Furthermore, the administration of SCF before drug administration allowed the dosages of taxol and vinblastine to be reduced by more than half, while retaining reductions in progenitor numbers that were unachievable using very high doses of the cytotoxic drug alone. Doxorubicin administration resulted in a 30- to 40-fold depletion in progenitors that was not significantly altered by preceding SCF administration. These results suggest that previous observations of in vivo selection using MDR1 gene transfer followed by taxol administration may have resulted from selection at the level of relatively mature, nonclonogenic precursor cells. Furthermore, these data suggest that cytokine prestimulation may be a useful strategy for improving the selection of drug-resistant clonogenic progenitors and, possibly, stem cells in vivo.