Coronary artery disease is a major socioeconomic problem in industrialized as well as in developing countries. Thus, many research efforts continue to address the identification of acquired and inherited risk factors of this complex disease. Recent advances in genotyping technology have made available newer and more powerful tools for the identification of susceptibility genes that in turn may provide new opportunities to evaluate the individual cardiovascular risk profile, detect novel disease pathways, and develop innovative therapeutic approaches. Replication of results is essential to establish unequivocally the impact of genetic variants in complex diseases. At the moment, only distinct but tightly linked single nucleotide polymorphisms on chromosome 9 have been consistently shown to be associated with different clinical phenotypes of coronary artery disease.