Atherosclerosis (As) is a chronic inflammatory disease, which is the common pathological basis of many cardiovascular and cerebrovascular diseases. But the pathological procedure involved is complicated, and the molecular mechanism is still unclear. In recent years, microarray, proteomics, High-throughput sequencing and metabolomics are used widely, helping us further understand the molecular mechanism. At the same time, the rapid development of bioinformatics largely speeds up the requirement and analysis of biomedical data. Among this, the pathogenesis of atherosclerosis is gradually recognized, including atherosclerosis genomics, proteomics, metabonomic and drug target prediction and so on. This revealed that inflammation, immunity, oxidative phosphorylation, lipid metabolism and energy dysfunction were highly correlated with the pathogenesis of atherosclerosis. This review will discuss the applications of bioinformatics in As.