Injury and endothelial cell apoptosis are hall marks of atherosclerosis (AS). However, the mechanisms underlying its pathogenesis remain ill-defined. Recent evidence of a role for microRNAs in AS-associated endothelial cell apoptosis encouraged us to address this question. Here, AS was developed in ApoE (-/-) mice supplied with a high-fat diet (HFD), compared to ApoE (-/-) mice supplied with a normal diet (ND). Mouse endothelial cells were isolated from the aortic arch using flow cytometry based on their expression of CD31. Human aortic endothelial cells (HAECs) were treated with oxidized low-density lipoprotein (ox-LDL) as an model for AS. Gene expression was quantified by RT-qPCR and protein levels were analyzed by Western blotting. Apoptosis was evaluated by FITC Annexin V Apoptosis assay and by TUNEL staining. Predicting binding patterns between miRNAs and the 3'-UTR of mRNA from the target gene was performed by bioinformatics analyses and confirmed by a dual luciferase reporter assay. We found that HFD mice, but not ND mice, developed AS in 12 weeks. A significant reduction in endothelial cells and a significant increase in mesenchymal cells were detected in the aortic arch of the HFD mice, compared to those of ND mice. Endothelial cell apoptosis was significantly higher in HFD mice, seemingly due to functional suppression of protein translation of anti-apoptotic Bcl-2 protein through upregulation of miR-1907, confirmed by analysis. Moreover, inhibition of miR-1907 abolished the effects of ox-LDL-induced apoptotic cell death on HAECs. Thus, AS-associated endothelial cell apoptosis may partially result from downregulation of Bcl-2, via upregulation of miR-1907 which binds and suppresses the translation of Bcl-2 mRNA.