Chromosomal translocation-generated fusion genes in childhood acute lymphoblastic leukemia (ALL) are well-known indicators of prognostic outcome. This study was conducted to establish the clinical relevance of the fusion genes distribution pattern in Mexican children with newly diagnosed ALL. Multiplex RT-PCR assays were used to detect 4 commonest fusion transcripts in 261 Mexican children with B-cell precursor ALL aged 1 to 14 years old, comparing differences in the distribution of the patients between molecular subgroups to a common collection of clinical parameters. We documented a 13% significant proportion of all patients who are more than 10 years of age, harboring fusion transcripts associated with leukocytosis and poor response to remission-induction chemotherapy, than those negative children for chimeric transcripts (P<0.001). Most notable observation was identified a significant number of e2a-pbx1-positive patients who showed a more aggressive disease at diagnosis. As presented here, this report gives an overview of the clinical implications of the fusion gene positivity in Mexican children with ALL in the context of traditional risk stratification variables. Our data support the existence of important ethnic and geographic differences in Mexican population.