Polyaspartoyl l-arginine (PDR) is an anti-thrombotic agent and its anti-thrombotic effect is related with endothelial cells. This study is to investigate the effect of PDR on the endothelial cells. In cell injury assay 1.7–170 μg/ml of PDR significantly increased the viability of rat aorta endothelial cells (RAECs) injured by H2O2, this effect was comparable with that of 95 μg/ml of α-tocopherol, and was more powerful than that of l-arginine. Nitric oxide synthase(NOS) inhibitor, L-NAME, almost abolished the effect of PDR, but not influence the effect of α-tocopherol or l-arginine. PDR enhanced the viability of RAECs injured by oxidized- low density lipoprotein (ox-LDL) either, which was comparable to that of α-tocopherol, whereas l-arginine, l-aspartic acid alone or their combined use failed to showed effects. PDR (17–170 μg/ml) raised nitrite level in RAEC medium, which is the major end-product of NO, but l-arginine (170 μg/ml) produced insignificant nitrite level rise. In addition, in the absence of RAEC PDR and l-arginine but α-tocopherol failed to lower the concentration of oxidative product (Fe3+) in a cell free system, whereas in the presence of RAEC PDR, l-arginine or α-tocopherol all significantly reduced the concentration of Fe3+. In cell apoptosis assay PDR (17–170 μg/ml) lowered the percentage of early apoptotic and late apoptotic RAECs, consequently increased the percentage of normal cells. Furthermore PDR significantly inhibited caspase-3 activity in RAECs; this effect is comparable with α-tocopherol and more potent than that of l-arginine. In conclusion, PDR is a cell protector, it protects endothelial cell against oxidative injury and apoptosis; its cell protective effect against H2O2 injuries is NOS dependent and is related with NO production; PDR is anti-oxidant, its anti-oxidant effect needs endothelial cell's participation. The findings suggest PDR may play a much better beneficial role than l-arginine in the prevention and treatment for those diseases with endothelial dysfunction.