Standard therapy for acute myeloid leukemia (AML) consists of hematopoietic cell transplantation (HCT) including autologous-HCT (AUTO) and allogeneic-HCT from a matched-sibling donor (MSD) or well-matched unrelated donor (WM-URD). When a conventional donor is not available, HCT from a partially-matched (PM)-URD or familial-mismatched donor (FMMD) is typically considered. We analyzed 561 patients with intermediate to poor-risk molecular cytogenetics who underwent transplant from 2002 to 2013 in their first remission. Engraftment was successful in all donor types except five patients who died in aplasia. Disease-free survival (DFS) at 5 years was 61.4% for MSD, 62.1% for WM-URD, 65.3% for FMMD, 44.7% for AUTO and 36.8% for PM-URD. AUTO showed the highest relapse rate (51.0%) compared to MSD (23.5%) and FMMD (18.5%), but showed the lowest 5-year non-relapse mortality (NRM) rate (3.8%). PM-URD showed the highest NRM (29.3%) with more instances of acute graft-vs.-host disease (GVHD) with grade≥III (29.3%), compared to MSD (15.6%) and FMMD (15.7%). In a poor-risk subgroup, the 5-year DFS for FMMD and MSD was 59.8% and 46.7%, respectively, while for AUTO and PM-URD it was 12.6% and 0.0%, respectively, which was caused by a high relapse rate (87.1% in AUTO, 83.3% in PM-URD). In the intermediate-risk subgroup, the 5-year DFS of AUTO (53.9%) was not different from the conventional donors in multivariate analysis, presenting a low NRM rate (5.1%). FMMD should be considered prior to PM-URD in intermediate-to-poor-risk AML and GVHD prophylaxis should be intensified when PM-URD is needed. AUTO might be considered for selected patients in the intermediate-risk group.