Autoimmune diseases are associated with increased cardiovascular (CV) risk, not only in consequence of specific disease-driven autoimmune processes targeting the vessels and the heart, but also because of accelerated atherosclerosis. The latter itself is a complex multifactorial process influenced by both classical and autoimmune disease–associated risk factors. Notwithstanding the increasing awareness of the problem, cardiovascular disease prevention and management in autoimmune disorders are still insufficient. The complex and peculiar lipid metabolism disturbances demonstrated in autoimmune patients raise uncertainty on the use of the classical lipid indexes for CV risk calculation and on the usefulness of lipid-lowering drugs. Treatment of lipid disturbances in autoimmune diseases at present is based on: control of disease activity, which should be obtained through a careful choice of the less atherogenic drugs as possible; modulation of serum lipoprotein levels with healthy lifestyle/diet, nutraceuticals, and drugs; modulation of lipoprotein functions with healthy lifestyle/diet, nutraceuticals, and drugs.