Atherosclerosis is a complex disorder that involves several mechanisms of pathogenesis tightly related to each other: lipid accumulation, inflammation and structural changes in the arterial wall. The main source of lipids accumulating in the arterial wall is low-density lipoprotein (LDL) atherogenically modified by desialylation or oxidation. Oxidized LDL can be produced as a result of enhanced generation of reactive oxygen species by mitochondria during oxidative stress. Mitochondrial dysfunction was found to be involved in every aspect of atherosclerosis, and is currently evaluated as a potential point of therapeutic intervention. In particular, atherosclerosis-associated inflammation and its link to mitochondrial dysfunction appear to be interesting, since mitochondria not only trigger the response to external signals, but also can act as pro-inflammatory agents themselves. In this regard, atherosclerosis is potentially an autoimmune disease. In this review, we summarize recent insights on the role of mitochondrial dysfunction in atherogenesis and discuss the significance of mitochondria for understanding of molecular basis of cardiovascular diseases.