Chronic myeloid leukemia (CML) is thought to arise from a pluripotent hematopoietic stem cell that has undergone a reciprocal translocation between the BCR gene on chromosome 22 and the ABL proto-oncogene on chromosome 9. This rearrangement results in a shortened chromosome 22, designated the Philadelphia (Ph) chromosome. The Ph chromosome has been found in cells from all hematopoietic lineages except mature T lymphocytes. To examine this issue, we combined fluorescence-activated cell sorting (FACS) and fluorescence in situ hybridization (FISH) to study lineage involvement of mature cells and stem cells in 12 patients with CML in the chronic phase. We found Ph chromosomes in myeloid cells and most B lymphocytes (CD19(+)) but not in mature T cells (CD3(+)) or natural killer (NK) cells (CD3(-)56(+)). Moreover, evidence of BCR/ABL fusion was found in pluripotent stem cells (CD34(+)Thy-1(+)), B-progenitor cells (CD34(+)CD19(+)), T/NK progenitor cells (CD34(+)CD7(+) cells), and T progenitor cells (CD34(+)CD7(+)CD5(+)) with a frequency equal to that in all CD34(+) cells isolated by FACS from bone marrow cells. T lymphocytes showed a marked decrease in Ph+ cells between progenitor cells and mature cells. Moreover, the ratios of Ph+ to Ph- cells in mature T cells and NK cells were below background levels, whereas Ph+ B lymphocytes also decreased during their maturation. These data suggest that Ph+ lymphocytes are eliminated during differentiation. In contrast to FISH of blood and bone marrow, which gives information principally about mature cells, the technique of "sorter FISH (FACS + FISH)" provides a powerful tool to explore the cytogenetic changes in immature cell populations of stem cell diseases based on immunophenotypes. Further clarification of genetic changes in stem cells could be achieved by using sorter FISH with monoclonal antibodies.