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Vaccarin (VAC), an active flavonoid glycoside from vaccariae semen, exhibits extensive biological activities including vascular endothelial cell protective effects. Histone deacetylase1 (HDAC1) is an epigenetic regulator in cellular apoptosis. In this study, we evaluated the protective effects of VAC on high glucose (HG)-induced cell apoptosis in human microvascular endothelial cells (HMEC-1). The levels of reactive oxygen species, activities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) were measured. Expressions of HDAC1, Bax, Bcl-2, caspase-3 and cleaved caspase-3 were detected with western blot. Flow cytometry was used to determine cell apoptosis and cell cycle. We found that HG treatment decreased cell vitality, upregulated HDAC1 protein level, promoted reactive oxygen species production, induced cell cycle arrest and cell apoptosis in HMEC-1 cells, which were all rectified by VAC. Both scavenging reactive oxygen species and inhibition of HDAC1 alleviated the apoptosis of HMEC-1 cells in response to HG. Pretreatment with VAC prevented HG-stimulated reactive oxygen species generation and HDAC1 expression in HMEC-1 cells. Taken together, these data suggested that VAC protected against HG-induced endothelial cell apoptosis via inhibition of reactive oxygen species accumulation and HDAC1 expression. VAC may be a potential therapeutic agent for treatment of diabetes mellitus (DM)-related endothelial dysfunction.Schematic model delineating the pathway wherein VAC protects against HG-induced endothelial cell apoptosis.