Cytogenetic analysis yields important objective information that has been shown to correlate with both patient response to therapeutic intervention and patient survival. Bone marrow samples are submitted to a common reference laboratory for cytogenetic analysis from children with newly diagnosed acute lymphoblastic leukemia (ALL) registered on frontline Pediatric Oncology Group (POG) therapeutic studies (classification 8600 series). A portion of the sample from the Texas Children's Hospital (Houston, TX) a POG affiliate, was also submitted to a local cytogenetics laboratory for analysis. This study retrospectively compares karyotypic data and methods from the Laboratory of Medical Genetics, University of Alabama at Birmingham (reference laboratory) with those of the Kleberg Cytogenetics Laboratory at the Baylor College of Medicine (local laboratory) over a 35-month period to evaluate the effect of differences in specimen procurement, handling, and laboratory methodology on yield of cytogenetic information. Each laboratory was able to identify clonal abnormalities in 72% of cases examined during the last year of the study. When these data were combined, the overall detection rate of clonal abnormalities was 87.5%. Utilizing the same bone marrow aspirate from 73 children, this study demonstrates that cytogenetic methodology significantly affects the yield of identifiable clonal abnormalities, while variables such as overnight shipping have no discernable effect. This study also supports the contention that central laboratory testing effectively yields information critical to ongoing large-scale research endeavors.