Residual disease (RD) is one of the risk factors for relapse after hematopoietic stem cell transplantation (HSCT) in hematological malignancies. Although recent advances in the technology for detecting minimal/measurable RD, such as multiparameter flow cytometry and quantitative PCR, enable risk stratifications of disease relapse, these examinations still have limitations in routine clinical practice. In this study, we assessed RD in bone marrow (BM) specimens on day 0 of allogeneic HSCT by immunostaining of case-specific leukemic blast markers and analyzed the relationship between day 0 BM status and HSCT outcomes. We analyzed 82 adult HSCT recipients with myeloid malignancies. BM histology of day 0 revealed almost empty marrow with a small number of residual BM cells. However, residual blasts could be detected by immunostaining even for only a few cells. When patients were divided into two groups according to the existence of RD on day 0, those with positive RD showed significantly lower overall survival rate (27% vs. 73%, P<0.001) and higher cumulative incidence of relapse (46% vs. 9%, P=0.006) at one year compared to those with negative RD. Furthermore, even if they were not in remission at the point of the pre-conditioning evaluation, the patients who achieved negative RD on day 0 showed comparable prognosis with those who maintained remission before conditioning. This study shows the efficacy of day 0 BM pathology of allogeneic HSCT as a prognostic factor that can contribute to clinical decisions on post-transplant strategies.