Coronary heart disease (CHD) is one of the main leading causes of death worldwide. CHD is a complex condition resulting from numerous gene-gene and gene-environment interactions. A large number of candidate genes exist. We review the evidence for the role of apolipoprotein E, lipoprotein lipase and interleukin-6 in CHD and their interaction with smoking (an environmental risk). The main objective of genetic research into CHD is to provide a complete risk assessment, complementing the well-studied traditional clinical and biochemical risk factors. Unravelling the role that functional gene polymorphisms play in determining risk, and in determining the levels of intermediate phenotypes is crucial to our understanding of the key metabolic pathways and physiology not only in the diseased, but also in the disease-free state. The identification of new molecules (implicated in the relevant metabolic pathways) may subsequently lead to potential targets for therapeutic intervention. Improving our molecular understanding may also lead to the development of improved diagnostics. Sequencing of the entire genome is now a reality. Advances in technology, such as the development of "gene chips" may allow us to study 100 000 genes at a time on a single chip. Such advances will amplify the power available to us in the realms of research into genetic physiology and interaction with environmental stimuli. The insights that these novel approaches may yield are eagerly awaited.