To examine the diagnostic value of serum ferritin, the associated risk factors, and cytokine profiles of hemophagocytic syndrome (HPS) following allogeneic hematopoietic cell transplantation (allo-HCT), we retrospectively analyzed data from patients undergoing allo-HCT between 2006 and 2012. Of 223 eligible patients, 18 patients developed HPS. A serum ferritin level above 30,000 μg/l was highly specific for the detection of HPS (specificity, 93%). The one-year survival rate for HPS was significantly lower than that of non-HPS patients (37.5% vs. 72.9%, respectively, Log-rank p < .01). In multivariable Cox models, antigen mismatches in human leukocyte antigen (HLA) in both graft-versus-host (GVH) and host-versus-graft (HVG) directions were significantly associated with the incidence of HPS. We found a significant elevation of Th1 cytokine (IFN-γ), Th2 cytokines (IL-10), and chemokines (MCP-1 and IP-10), at the onset of HPS. Our results suggest that allo-reactivity, derived from HLA-mismatch, and possibly causing a cytokine storm, may be associated with HPS development.