To evaluate the prognostic significance of Wilms' tumor gene 1 (WT1) expression for monitoring minimal residual disease and predicting relapse in patients with acute leukemia (AL) following allogeneic hematopoietic SCT (allo-HSCT), the WT1 expression levels of 138 AL patients were measured using real-time quantitative reverse transcription PCR at designed time points after allo-HSCT. All patients were divided into four groups based on the HSCT outcomes and intervention application. A low level of WT1 expression following HSCT indicated a low risk of relapse, whereas WT1 expression 41.05% was indicative of a higher probability of relapse. Only the advanced stage of disease (hazard ratio (HR) ¼ 2.73; 95% confidence interval (CI) ¼ 1.337-5.573, P ¼ 0.006) and a WT1 expression X0.60% (HR ¼ 4.774; 95% CI ¼ 2.410-9.459, P ¼ 0.000) were associated with lower disease-free survival. Relapse (HR ¼ 0.119; 95% CI ¼ 0.056-0.250, P ¼ 0.000) and a WT1 expression X0.60% (HR ¼ 2.771; 95% CI ¼ 1.316-5.834, P ¼ 0.007) were associated with lower OS. In conclusion, the WT1 expression level is an independent prognostic factor that can predict clinical outcomes for AL patients after HSCT and provide a guide for suitable interventions.