OBJECTIVE: To study the relationship between bone marrow relapse and the level or changes of minimal residual disease (MRD) in childhood acute lymphoblastic leukemia (ALL). METHODS: The MRD level was detected using the modified limiting dilation PCR and nested PCR in 46 children with ALL; the data was analyzed using the Kaplan Meier method and COX model. RESULTS: The MRD level of the 46 patients by the time of complete remission (CR) was positively correlated with marrow relapse (r= 0.4396 ,P< 0.05 ). There was a significant difference in the MRD level between marrow relapse children and non relapse children ( 7.359 ×10 -3 vs 3.954 ×10 -4 ; P< 0.05 ). The cases whose MRD was persistently positive or changed from negative to positive during CR had a higher relative risk for relapse (P< 0.05 ). CONCLUSIONS: The MRD level by the time of CR and the qualitative findings in the period of CR are important markers in accessing the prognosis in childhood ALL. MRD detection by PCR can be used to identify the relative risk for relapse and make more effective treatment and prophylaxis regimens for relapse in childhood ALL.