Despite comparable outcomes of haploidentical transplants (Haplo-HSCT) with HLA-matched unrelated transplants (MUD-HSCT) in retrospective comparisons, few studies have prospectively compared Haplo-HSCT with MUD-HSCT in AML. Here, we prospectively compared the outcomes of Haplo-HSCT with MUD-HSCT for AML in remission (n=110) to prove non-inferiority of overall survival in Haplo-HSCT. Both groups were well balanced in factors related to biological features of AML and measurable residual disease (MRD) status by Wilms' tumor gene 1 (WT1) assay. A unique reduced-toxicity preparative regimen was used for Haplo-HSCT, whereas mostly myeloablative regimens for MUD-HSCT. Both groups showed similar patterns of neutrophil and platelet recovery, whereas delayed T cell reconstitution in Haplo-HSCT compared with MUD-HSCT. No significant differences were found in acute or chronic graft-versus-host-disease (GVHD) and post-transplant infectious events with an exception of EBV or CMV infection, which occurred more frequently in Haplo-HSCT. After a median follow-up of 47 months, no significant differences in overall survival (65% versus 54%, P=0.146), disease-free survival (67% versus 53%, P=0.142), relapse (20% versus 21%, P=0.858), non-relapse mortality (14% versus 26%, P=0.103), and GVHD-free/relapse-free survival (54% versus 41%, P=0.138) were observed for Haplo-HSCT versus MUD-HSCT. In multivariate analysis, WT1 expression before transplantation independently predicted relapse, resulting in inferior survival. Separate analysis of unenrolled patients (n=110) who were excluded or refused to participate in this study showed consistent results with enrolled patients. This prospective study demonstrated the non-inferiority of Haplo-HSCT to MUD-HSCT for AML in remission and validated the role of WT1 quantification as an MRD marker (ClinicalTrial.gov identifier: NCT01751997). This article is protected by copyright. All rights reserved.