Common complex diseases, such as psychiatric disorders, cancer, diabetes, heart disease and asthma, are caused by multiple genetic and environmental factors. Dissection of the genetic architecture underlying quantitative traits and complex disease is essential to our understanding of the aetiology of complex diseases that cause most of the disease burden in society. The nature of genetic variance for complex disease may be different to that of Mendelian disease. Whereas the latter are often caused by protein coding mutations, inherited gene variants may be involved in gene regulation. More specifically, genetic differences between individuals in quantitative traits, endophenotypes (phenotypes that are risk factors for disease) and susceptibility to common diseases may be caused by differences in gene expression at a number of loci. Therefore, understanding the genetic basis of gene expression is likely to lead to a better understanding of genetic variation of quantitative traits and risk factors for common diseases.