We report a patient with juvenile myelomonocytic leukemia who had two cytogenetically independent clones at the time of diagnosis. Fluorescence in situ hybridization analyses showed that 42.5% of myeloperoxidase(+) cells and 27.3% of CD20(+) cells had three signals for chromosome 8, while 13.1% of myeloperoxidase(+) cells and 6.0% of CD20(+) cells had del (Y). However, a great majority of CD3(+) cells had no numerical aberration of the two chromosomes. The two karyotypically abnormal clones might have developed from multipotential hematopoietic stem cells with the potential to differentiate into myeloid and B-lymphoid lineages, but not T-lymphoid lineage.