Intermittent high glucose (IHG), one of the general and important symptoms of patients with diabetes, has greater effect than sustained high glucose on the development of diabetic cardiovascular complications, in which endothelial dysfunction caused by oxidative stress is regarded as the initiation. However, no study investigated either the degree of endothelial DNA oxidation caused by IHG or the potential protective effects of antioxidants. In this study, DNA oxidation, including 8-hydroxy-2'-deoxyguanosine (8-OHdG) concentration and comet assay, was studied in human umbilical vein endothelial cells (HUVECs) under IHG with or without treatment of Ginkgo biloba extract (EGb 761). We found that high glucose, especially IHG, increased reactive oxygen species generation, 8-OHdG content and oxidative DNA damage in HUVECs. These high glucose-induced oxidative stress could be suppressed by EGb 761 (25-100 microg/ml) in a dose-dependent manner through the improvement of total antioxidant capacity. Our results indicated that the presence of significant DNA oxidation in HUVECs exposed to high glucose, and especially higher in the cells in IHG conditions. EGb 761, an antioxidant herbal medicine, can remarkably alleviate endothelial DNA oxidation caused by IHG, which may provide a novel approach for endothelial protection in the presence of IHG.