Hematopoietic stem cell transplantation (HSCT) involves the potential for certain serious transplant-related complications such as graft-versus-host disease (GVHD), and recovery from such complications is vital for a successful HSCT outcome. Acute GVHD (aGVHD) occurs in the early period after transplantation and is initiated by alloreactive donor T cells. The mechanisms whereby immune responses trigger this post-transplantation condition remain unclear, but endothelial cell function might play a role in this. We investigated the expression of endothelial cell activation markers such as sE-selectin, sVCAM-1, PAI-1 and microparticle (MP) in patients undergoing allogeneic HSCT. Additionally, we studied the effects of recombinant soluble thrombomodulin (rTM) on the expression of these markers. Our study cohort included 312 patients who underwent allo HSCT at 25 institutions in Japan. In the 143 patients who developed aGVHD, levels of endothelial cell activation markers were significantly higher compared to patients who did not develop aGVHD. Moreover, patients who received rTM exhibited a significantly lower frequency of aGVHD and reduced levels of endothelial cell activation markers. Our findings suggest that endothelial cell activation might be linked to aGVHD, and that rTM might at least in part act to prevent aGVHD by its effect on endothelial cells.