Background: Aberrant DNA methylation of promoter-associated cystosine-guanine islands is known to play an important role in leukemogenesis and has been reported to have association with poor prognosis in acute lymphoblastic leukemia (ALL). In adult, residual methylation at clinical remission status in patients with acute myeloid leukemia and Philadelphia chromosome-positive ALL showed significant association with poor prognosis in recent studies. We analyzed 47 patients with childhood ALL to evaluate the change of methylation status from the time of diagnosis to the time at morphologic remission. Methods: We analyzed the methylation status of CDH1, p16 and DAPK genes in 47 patients using methylation specific polymerase chain reaction method with genomic DNA extracted from bone marrow (BM) aspirates. All patients were treated with standard chemotherapy and after 4 weeks, every patient achieved morphologic complete remission. Methylation status of above three genes were also analyzed with the same method in 10 BM aspirate samples from healthy BM donor for comparison. Results: CDH1 was methylated in 30 (64%) patients, p16 in 2 (4%) patients and DAPK in 6 (13%) patients at the time of diagnosis. Thirty (70%) patients had methylation at least one gene, and 5 (11%) had methylation of 2 genes. None of the healthy BM donors showed methylation of above genes. At the time of morphologic remission, all patients who had aberrant DNA methylation of any gene at the time of diagnosis had no detectable residual methylation showing complete resolution of aberrant DNA methylation of examined genes. Clinical prognostic factors including initial white blood cell count, immunophenotype and presence of specific translocations (TEL-AML1, BCR-ABL, E2A-PBX1) did not show any association with initial methylation status. Age was the only factor which showed correlation with methylation status; patients under 2 year old showed significantly low frequency of methylation of above three genes (p 0.001). Conclusion: Since aberrant DNA methylation of CDH1, p16 and DAPK genes were found in 70% of pretreatment ALL patients and none in healthy BM donor showing complete resolution of methylation at morphologic remission status, we cautiously suggest aberrant DNA methylation as a potential biomarker reflecting disease status in childhood ALL.