Objective: To investigate the clinical significance of monitoring ETV6-RUNX1 fusion gene in children with acute lymphoblastic leukemia (ALL) after allogeneic stem cell transplantation (allo-HSCT) . Methods: Clinical data of 13 children received allo-HSCT in Peking University Institute of Hematology from May 2009 to March 2016 were retrospectively collected. The ETV6-RUNX1 gene was examined by real-time quantitative polymerase chain reaction (RQ-PCR) . The correlation between its expression level and the disease status was analyzed. Results: Of 13 enrolled ALL cases, the ETV6-RUNX1 expression of 7 patients converted to positive after transplant at a median time of 137 days (range, 28-270 days) . The expression level of the first positive sample was 0.034% (range, 0.004%-0.061%) . The duration from ETV6-RUNX1 positive to hematological relapse was 196 days (range, 28-666 days) . Four patients experienced relapse at a median time of 294 days (range, 104-803 days) after allo-HSCT. The ETV6-RUNX1 expression converted to positive prior to MRD. Patients with positive ETV6-RUNX1 gene expression pre-transplantation would be more likely to relapse. Conclusion Monitoring ETV6-RUNX1 by RQ-PCR could be used to evaluate MRD status after allo-HSCT. Patients with positive ETV6-RUNX1 after transplant had a poor prognosis.