HSCT is the only proven treatment option for CML, a rare disease in children. Recently, there are promising reports on the advantageous effect of imatinib mesylate for pediatric patients with CML. We conducted a retrospective study on 33 pediatric patients suffering from CML. Fourteen underwent HSCT and the rest were treated with imatinib. With a median follow-up of 24 months, the two-yr OS in the HSCT group and the imatinib group was 84% and 87%, respectively (p = 0.714). The probabilities of two-yr DFS were 59% in the HSCT group and 82% in the imatinib group, either (p = 0.880). Relapse occurred in 5 (35.7%) patients of the HSCT group, and 8 (42.1%) patients showed relapse in the imatinib group. Among nine patients who died, five were in the HSCT group and the rest were in the imatinib group. The probability of relapse in the patients of the imatinib group followed up for several consecutive years may be higher than observed in the HSCT group, so we cannot easily conclude which way is more reliable.