Damage to endothelial cells is the common feature of vascular disorders associated with hematopoietic stem cell transplantation (HSCT). Elevated numbers of circulating endothelial cells reflect the extent of endothelial damage in a variety of disorders but their use in HSCT has not been investigated so far. We studied 39 patients undergoing allogeneic HSCT with different conditioning regimens and 22 healthy controls. Circulating endothelial cells were enumerated with immunomagnetic isolation during the course of HSCT. After conditioning, cell numbers were significantly elevated (median 44 cells/mL) compared with baseline (median 16 cells/mL) and controls (median 8 cells/mL). Patients who received radiation had an earlier peak when compared with patients who received chemotherapy. Patients who received reduced-intensity conditioning had significantly lower cell numbers (median 24 cells/mL) than those who received standard conditioning. These observations provide a novel marker to investigate microvascular endothelial damage and the effects of different conditioning regimens in patients undergoing HSCT.