Cell-derived microparticles (CDMP) appear to play an important role in thrombosis and hemostasis. However, the role of CDMP in the development of transplant-related complication after allogeneic SCT is poorly understood. We investigated the significance of CDMP such as platelet-derived (PDMP) and endothelial cell-derived (EDMP) in patients undergoing allogeneic SCT. In addition, we measured and compared the levels of cytokines and soluble factors in these patients. The subjects were 31 patients who underwent allogeneic SCT. Most of the cytokines/soluble factors exhibited a significant elevation after allogeneic SCT. When the relationship between CDMP and cytokines/soluble factors was analyzed, EDMP levels correlated positively with sIL-2R, sVCAM-1, sE-selectin, PAI-1 and sFasL. However, IL-6 was not correlated with EDMP. In contrast, PDMP levels correlated positively with IL-6, PAI-1, sVCAM-1 and sE-selectin, but not with sIL-2R and sFasL. In addition, the patients with high-grade GVHD exhibited a significant increase in EDMP compared to patients with low-grade GVHD. Our results suggest that PDMP and EDMP participate in the procoagulant activity after allogeneic SCT. Furthermore, EDMP also plays an important role in symptoms related to GVHD after allogeneic SCT.