Juvenile chronic myelogenous leukemia (JCML) is a heterogeneous disorder composed of Philadelphia chromosome-positive (Ph+) CML, which is similar to CML in adults, and Ph-negative (Ph-) CML, a childhood myelodysplasia resembling chronic myelomonocytic leukemia in adults. These two disorders are not always readily separable by leukocyte alkaline phosphatase (LAP) scoring and by karyotyping, yet they have different courses and outcomes. We compared the results of breakpoint cluster region (bcr) gene rearrangement analysis with LAP score and karyotype in these patients. In addition, analysis for immunoglobulin and T-cell receptor gene rearrangement was done to investigate the possibility of mixed myeloid and lymphoid lineage, which has been shown to occur in childhood acute myelogenous leukemia and CML in blast crisis. Peripheral blood and bone marrow samples from six patients with JCML aged 5 to 19 yr were analyzed. One case was Ph+, and five were Ph- by karyotyping. Two samples showed LAP scores of 5 and 11 (one Ph+ and one Ph-); others were normal. All were digested with EcoRI, HindIII, and BamHI for immunoglobulin heavy and light chains and T-cell receptor beta-chain analysis and, in addition, with BglII for bcr analysis. Samples were hybridized with probes to JH, JK, CT beta, and bcr (Oncor). A bcr rearrangement was shown in the Ph+ sample; all others, including one with a very low LAP score, were negative. No JH, JK, or CT beta rearrangements were detected.(ABSTRACT TRUNCATED AT 250 WORDS)