Coronary artery disease (CAD) including myocardial infarction (MI) is a common disease and among the leading cause of death in the world. The onset of CAD depends on complex interactions of environmental and genetic factors. To clarify the genetic architecture of MI, we started a genome-wide association study (GWAS) using nearly 100 000 gene-based single-nucleotide polymorphisms (SNPs) from 2000, and identified LTA associated with the increased risk of MI in Japanese population. To our knowledge, this is the first study identified a genetic factor for common disease by GWAS in the worldwide. Through examining the LTA cascade by combination of molecular biological and genetic analyses, we have identified additional MI susceptible genes, LGALS2, PSMA6 and BRAP, so far. Nowadays a lot of large-scale GWAS have identified numerous genetic risk factors for common diseases. In CAD, 51 loci with GWAS significance (P<5 × 10−8) have collectively identified by recent large-scale GWAS mainly in Caucasian descent. In this review, we discuss recent advances in molecular genetics for CAD.