OBJECTIVE: To identify the expressed sequence tags (EST) associated with childhood acute lymphoblastic leukemia (ALL) at chromosome 6q16.3, so as to clone candidate genes at the locus. METHODS: The expression of EST at 6q16.3 in lymphocytes was detected using EST homology analysis in bioinformatics along with reverse transcription-polymerase chain reaction in 10 children with ALL and 5 healthy children. RESULTS: The EST AA403058 expression decreased in seven of ten ALL children compared with that in healthy children (P<0.001). CONCLUSIONS: The EST AA403058 expression is down-regulated in childhood ALL, suggesting it may be involved in the development of childhood ALL. This study provided important information toward cloning childhood ALL associated genes.