Endostatin (ES) was reported to stimulate apoptosis in endothelial cells, but the exact mechanism remains controversial. In the present study, we elucidate the mechanism of ES-induced endothelial cell apoptosis. Our results indicate that ES induces cytochrome c release and caspase-9 activation in human microvascular endothelial cells (HMECs) at the concentration of 1 µM for 24 h, which initiates the apoptosis process. Further, ATP production, mitochondrial membrane potential, and tubule formation assays showed that ES promotes the mitochondrial permeability transition pore (mPTP) opening via voltage-dependent anion channel 1 (VDAC1), a major component of mitochondrial outer membrane. Knocking down VDAC1 by small interfering RNA attenuates ES-induced apoptosis, while overexpression of VDAC1 enhances the sensitivity of endothelial cells to ES. Moreover, we reveal that ES induces the reduction of hexokinase 2 (HK2), which, in turn, promotes VDAC1 phosphorylation and accumulation. Data from two-dimensional electrophoresis, immunoprecipitation, mPTP opening, and caspase-3 activation assays indicate that two serine residues of VDAC1, Ser-12 and Ser-103, can modulate VDAC1 protein level and thus the sensitivity to apoptosis stimuli. On the basis of these findings, we conclude that VDAC1 plays a vital role in modulating ES-induced endothelial cell apoptosis.—Yuan, S., Fu, Y., Wang, X., Shi, H., Huang, Y., Song, X., Li, L., Song, N., Luo, Y. Voltage-dependent anion channel 1 is involved in endostatin-induced endothelial cell apoptosis.