The observation that juvenile chronic myelogenous leukemia (JCML) and childhood bone marrow monosomy 7 syndrome (Mo 7) are similar in many clinical and epidemiologic respects suggests a shared pathogenic basis and raises the possibility that the bone marrows of patients with JCML might lose chromosome 7 alleles by mechanisms that do not result in detectable cytogenetic deletions. We used a series of polymorphic markers mapped to chromosome 7 to test this hypothesis in 22 children with MPS and MDS, including 19 with JCML. All MPS and MDS samples demonstrated allelic heterozygosity with at least one chromosome 7 marker; 16 were heterozygous with probes from both 7p and 7q. Furthermore, the percentage of patient bone marrow samples heterozygous at each locus tested was similar to the frequency observed in the normal population. Whereas these data demonstrate that submicroscopic loss of large segments of chromosome 7 alleles is uncommon in children with MPS and MDS who do not have Mo 7, they do not exclude small deletions around an uncharacterized tumor-suppressor locus. Our results suggest that a number of distinct molecular events contribute to leukemogenesis, and we propose a multistep model to explain the similarities and differences between the major subtypes of childhood MPS and MDS.