Abstract: Objective：To investigate the RUNX1-RUNX1T1 transcript (fusion transcript) dynamics in pediatric acute myeloid leukemia (AML) and their correlation with patients' clinico-biological characteristics and long-term outcomes. Methods：In a retrospective cohort, all patients with RUNX1-RUNX1T1-positive AML at Beijing Children's Hospital (our hospital), from October 1st, 2006 to March 31st, 2015 were enrolled. Patients were divided into high-expression or low-expression groups according to ＞104 copies, ＞103 copies, ＞102 copies, ＞10 copies, ＞1 copy and ＞0 copy per 104 copies GUS at diagnosis (time point 0, TP0) and following MRD detective time points, after Induction Ⅰ(TP1), Induction Ⅱ (TP2), and after ConsolidationⅠ (TP3), Consolidation Ⅱ (TP4) and Consolidation Ⅲ (TP5), respectively. The follow-up deadline was December 31st, 2017. Chi-square were used to test the differences of clinical and biological characteristics between the subgroups, Kaplan-Meier method was used to analyse patients' overall survival (OS) and relapse free survival (RFS), and Log-rank test for comparing the difference. Cox's proportional hazards regression model was used to analyze the independent significance for OS and RFS. Results：52 patients were enrolled and 27 of them were male, the median age was 8(2~14). Two patients were lost to follow up at TP1. 21 patients died during the follow-up, the median follow-up time of other 29 patients were 62.2(34~134.3) months. ①There were no significant differences in age, gender, WBC, Hb, PLT count, blasts account in the bone marrow, immunophenotype except CD15(P=0.004) and MRD of TP1~TP5 between the high-expression patients(17/50) and low-expression patients(33/50). ②Univariate analysis showed that RUNX1-RUNX1T1 transcript at TP1 and TP5 were corelated with 5 year OS and RFS, the gender and PLT count at TP0 were corelated with 5 year OS and WBC count at TP0 were corelated with 5 year RFS. Multivariate analysis showed that the RUNX1-RUNX1T1 transcript level ＞103 copies per 104 GUS at TP1 was the independent risk factor for poor OS of RUNX1-RUNX1T1+ pediatric AML patients, P=0.036, hazard ratio (HR) was 0.095 and the 95% confidence interval(CI) was (0.011, 0.860). Conclusion：The fusion transcript level after the first induction therapy was the independent factor affecting long outcome in RUNX1-RUNX1T1+ pediatric AML.