Abstract: A gene therapy system is disclosed that selectively kills leukemia cells in bone marrow, while leaving stem cells unaffected. All cells in a mixture of stem cells and leukemia cells are transfected with a high efficiency gene transfer vector. The vector carries a eukaryotic expression construct encoding a toxin gene. This toxin gene is expressed only in leukemia cells, not in stem cells. Differential expression of the toxin gene in leukemia cells and stem cells may be achieved by placing the coding sequence under the control of an appropriate promoter, such as the RSV promoter or the SV40 promoter. High gene expression has been demonstrated in a panel of transformed leukemia cell lines, but no gene expression in transformed, CD34-selected, primary human stem cells. The treatment will be useful not only for leukemia patients, but also for other cancer patients undergoing autologous bone marrow transplants (e.g., breast or lymphoma cancers).