OBJECTIVE: To study the role of minimal residual disease (MRD) in the evaluation of therapeutic effectiveness of childhood B-cell acute lymphoblastic leukemia (ALL)．METHODS: MRD testing was performed in 124 children with B-cell ALL, who were newly diagnosed and enrolled in the ALL-XH-99 treatment protocol from September 2001 to April 2005．MRD was determined by 4-color flow cytometry in the different time points during the treatment period．RESULTS: After induction therapy, 103, 13 and 8 patients showed MRD <0.01%, 0.01%-0.1% and >0.1%, respectively. The 5-year relapse-free survival (RFS) in the patients with MRD <0.01%, 0.01%-0.1% and >0.1% was 88.9±3.9%, 70.0±14.5% and 0%, respectively and the 5-year event-free survival (EFS) was 82.4±4.4%, 21.2±18.0% and 0%, respectively. There were significant differences in the RFS and EFS among the patients with different MRD levels (P<0.01). Within half a year after induction remission, the 5-year RFS in patients with MRD negative (<0.01%) and positive was 87.7±4.1% and 58.3±14.2%, respectively (P<0.01) and the 5-year RFS was 80.7±4.6% and 25.6±13.8%, respectively (P<0.01). After half a year with induction remission, the patients with MRD negative and positive also showed statistical differences in the 5-year RFS (92.0±3.6% vs 48.5±15.5%; P<0.01) and EFS (85.6±4.5% vs 21.4±11.0%; P<0.01). Multivariate analysis confirmed that the MRD level after induction chemotherapy together with the reaction to prednisone, the bone marrow features on the 19th day of induction, and the fusion gene with BCR-ABL or MLL-AF4 had prognostic significance in childhood B-cell ALL.CONCLUSIONS: The MRD level in the whole course of therapy is an important outcome indicator in childhood B cell ALL.