Several biologic systems contribute to the pathophysiology of atherosclerosis and its complications, and within each of these systems many genes have been explored to establish the possible implication of their variability in coronary heart disease (CHD) risk. This report is focused on recent results pertaining to lipid and inflammatory genes, their variability, and their relationship with intermediate phenotypes and CHD. For both systems, there is no evidence at the present time that testing genetic polymorphisms might be of any benefit to the patient, for the diagnosis or prognosis of CHD, or for tailoring drug prescription. Understanding the genetics of complex traits like CHD will require a system approach that allows a modeling of the interaction among genes as well as between genetic and nongenetic sources of variation.