While evidence for measurable residual disease (MRD) is a harbinger of inferior outcome in acute myeloid leukemia (AML) patients referred for allogeneic stem cell transplantation (allo-SCT), the exact clinical trajectory of specific patient subsets in this clinical setting is undefined. Using a recently published prognostic cytogenetic model (Leukemia 2019) we evaluated whether this model applied also to studies of patients with positive MRD. The analysis comprised MRD+ patients in first complete remission undergoing allo-SCT from a matched sibling donor or unrelated donor. Seven hundred and seventy-five patients were evaluated with a median follow-up duration of 22 months. Cytogenetic risk score was favorable, intermediate/FLT3wt intermediate/FLT3-ITD, and adverse in 15%, 28.3%, 37% and 19.7% of the patients, respectively. Favorable and intermediate/FLT3wt risk patients had 2-year leukemia-free survival rates of 78% and 61%, respectively, compared with only 50% and 37% for intermediate FLT3-ITD and adverse risk patients, respectively (p<0.0001). In multivariate analysis adverse and intermediate/FLT3-ITD risk patients were more likely to experience disease relapse compared with favorable risk patients [Hazard ratio (HR)=3.9, 95% confidence interval (CI), 2.1-7.3; p<0.0001, and HR=4.4, CI 95%, 2.4-7.8; p<0.0001, respectively]. The EBMT cytogenetic risk score is a valuable adjunct for risk stratification of MRD+ AML patients. This article is protected by copyright. All rights reserved.