Systemic lupus erythematosus (SLE) is a multisystem chronic autoimmune disease characterized by tissue inflammation. There is increased cardiovascular mortality in cases with SLE. Endothelial dysfunction is an early stage of atherosclerosis, which can be reversed early. We aimed to study noninvasive assessment of endothelial dysfunction in Egyptian patients with SLE. Three hundred individuals were recruited; 100 SLE patients with lupus nephritis (LN), 100 SLE patients free of LN as well as 100 healthy volunteers. The vascular endothelial function was evaluated through ultrasonographic assessment of brachial artery diameter to determine the flow-mediated dilation (FMD) as well as a blood endothelial marker called platelet endothelial cell adhesion molecule-1, also known as cluster of differentiation 31 (CD31), was measured. CD31 is abnormal in 93% of cases with LN and 79% in cases without nephritis. There was a significant higher level in CD31 in cases of LN compared with lupus without nephritis with P = 0.016. FMD is impaired in all cases with LN, 95% in cases without nephritis, and in 20% of the controls. There was a significant lower FMD in cases of LN compared with lupus without nephritis with P <0.001. Multiple regression analysis showed that FMD of the brachial artery (P <0.001) is an independent factor to predict LN. Endothelial dysfunction is increased in cases with SLE especially those with nephritis. CD31 and FMD can be used as noninvasive methods for early detection of endothelial dysfunction.