The effects of macrophage activation on the outcome of allogeneic hematopoietic SCT (allo-HSCT) have yet to be fully examined. A total of 70 adult patients who received a first allo-HSCT for hematological diseases were studied. We counted the number of hemophagocytic cells in BM clot sections on day þ 14±7, and analyzed its impact on subsequent outcome. In all, 23 patients were diagnosed as having increased numbers of hemophagocytic cells (HP group), whereas 47 were not (non-HP group). The HP group was not associated with an increased incidence of acute or chronic GVHD, but was associated with worse hematopoietic recovery than the non-HP group. The 2-year OS for the HP group and the non-HP group was 30 and 65% (Po0.01), respectively, and 2-year nonrelapse mortality was 48% and 27% (Po0.01), respectively. Multivariate analysis confirmed that the HP group was associated with a lower OS (hazard ratio (HR) ¼ 2.3; 95% confidence interval (CI), 1.0-5.4; P ¼ 0.048) and higher non-relapse mortality (HR ¼ 4.0; 95% CI, 1.6-9.9; Po0.01). The HP group had higher incidences of death due to graft failure (Po0.01) and endothelial complications, such as sinusoidal obstruction syndrome and transplant-associated microangiopathy (P ¼ 0.01). Macrophage activation is a previously unrecognized complication with negative impact on outcome of allo-HSCT.