Predicting severe acute GvHD (aGvHD) after allogeneic hematopoietic stem cell transplantation (HSCT) is challenging but critical. Mild aGvHD may have a favorable impact on relapse, whereas severe aGvHD is associated with poor outcomes. The aim of this study was to evaluate whether elevated eosinophil count in the bone marrow (BM) at 1 month after HSCT is associated with a high incidence of new and severe aGvHD. We enrolled 101 consecutive patients; median age was 50 years, and 50.5% patients were male. The median eosinophil concentration in BM at 1 month after HSCT was 1.1% (quartile 0.4–2.2%). The adjusted hazards ratio at 95% confidence interval for severe aGvHD was 1.26 (1.12–1.42, P<0.001), per 1% increase in eosinophil concentration, and 3.76 (1.41–10.05, P = 0.008) for the high-risk group at a cutoff value of 4.0%. In addition, the predictive accuracy described by area under the curve of receiver operating characteristics, increased from 0.784 to 0.866 (P = 0.033) with the increasing concentration of eosinophils. In conclusion, elevated concentration of eosinophils in BM was associated with high incidence and predictive accuracy of severe aGvHD. BM eosinophil concentration can be one of the key markers to predict aGvHD.