Different apolipoprotein combinations explain most of the functional differences between plasma lipoproteins. This emphasizes the pivotal role of apolipoproteins in the homeostasis and physiological control of lipid metabolism. Genetic polymorphisms of apolipoprotein (apo)A-I/C-III/A-IV, apoE and apoB have been suggested to modulate plasma lipid levels as well as the risk of coronary artery disease and stroke. Carotid artery intima-media thickness has been shown to represent preclinical atherosclerosis and has, therefore, been used as a surrogate in quantifying the early stages of atherosclerosis. The effects of the polymorphisms in apoA-I/C-III/A-IV and apoB on carotid intima-media thickness are poorly known. The corresponding influence of apoE polymorphisms has been studied more extensively, but the results are not yet conclusive. In this review, these results are presented in detail and the potential reasons and mechanisms for the discrepancies are discussed.