Atherosclerosis (AT) is a chronic autoimmune inflammatory disease, characterized by lipoproteins metabolism alteration leading to formation of pro-inflammatory and pro-oxidative lipids and immune response. Identification of macrophages, T cells, pro-inflammatory cytokines, adhesion cell molecules in atherosclerotic lesions support the hypothesis that innate and adaptive immune response participate in the atherogenesis mechanism. Multiple factors such as inflammatory, infectious and immune system, among others participate in this process. The principal antigens identified in atherogenesis are: oxidized LDL (oxLDL), HSPs and beta2GPI. During LDL oxidation, multiple neoantigens are formed (anti-EO). These antibodies seem to be protective. Systemic lupus erythematosus (SLE) and antiphospholipid syndrome (APS) have accelerated AT. The association of both diseases with AT suggests a common pathogenic mechanism. SLE and atherosclerosis are immune-complex mediated diseases. Participation of complement activation, and CD40, CD40 ligand interactions have been demonstrated in AT and SLE. AT may be the initial presentation or the consequence of primary antiphospholipid syndrome. The similarities between AT, SLE, and APS and the identification of protective antibodies offer opportunities for new immunomodulation treatment strategies.