OBJECTIVE: To evaluate the clinical significance of minimal residual disease (MRD) in childhood B-lineage acute lymphoblastic leukemia (B-ALL). METHODS: MRD was detected using triple-color flow cytometry (FCM) with a combination of specific and sensitive marker of cell plasma and membrance with CD45/SSC in 67 children with B-ALL at the end of the remission induction therapy. RESULTS: Of the 67 patients, 18 were low risk; 35, medium risk and 14 high risk. The MRD positive rate was significantly different among these patients with different degrees of risk. The high risk patients had the highest MRD positive rate, followed by the medium risk patients (P<0.05). MRD was not significantly correlated with the gender, age and the initial leukocyte counts, as well as with the response to early therapy. A significant association between MRD and the incidence of relapse as well as the event-free survival (EFS) period was observed. The relapse rate in patients with MRD positive was remarkably higher than that in those with MRD negative. The patients with MRD positive had a shorter EFS period compared with MRD negative patients. CONCLUSIONS: The detection of MRD can be used to evaluate the therapeutic effect and the prognosis of childhood ALL.