Objective: Preferential development of atherosclerotic lesions in areas of low shear stress is associated with increased endothelial inflammation, apoptosis and senescence. On the contrary, high shear stress areas are protected from plaque development, but the mechanisms remain elusive. Autophagy is a protective mechanism allowing recycling of defective organelles and proteins to maintain cellular homeostasis. Our aim was to understand the role of autophagy in athero-protective effects of high shear stress. Approach and Results: We used the parallel plate chamber system in vitro to generate different shear stress conditions on endothelial cell deficient or not in autophagy (shRNA Atg5 vs. control) and examined autophagic flux in cells transfected with RFP-GFP-LC3 plasmid. Endothelial autophagy was silenced in Atg5 flox/flox ; VE-cadherin-cre mice. We first demonstrated in human and murine arteries and in cultured endothelial cells that atheroprotective shear stress activates endothelial autophagic flux. On the opposite, endothelial cells exposed to atheroprone low shear stress displayed inefficient autophagy, associated with activation of mTOR, inhibition of AMPKα pathways and blockade of the autophagic flux. Interestingly, plaque burden augmented specifically in areas usually atheroresistant in ApoE -/- hypercholesterolemic mice deficiency in endothelial autophagy. Both in cultured endothelial cells and in transgenic mice, deficiency in endothelial autophagy was associated with a defect in endothelial alignment with flow direction, a hallmark of endothelial cell health. Deficiency in endothelial autophagy increased endothelial senescence and TNFα-induced inflammation under high shear stress conditions. These effects were associated with impaired KLF2 activation. In transgenic mice, endothelial senescence and apoptosis was augmented in high shear stress areas of the descending thoracic aorta when compared to control littermate mice. Conclusions: Altogether, these results show that adequate endothelial autophagic flux under high shear stress limits atherosclerotic plaque formation by preventing inflammation, senescence and apoptosis.