The advent of advanced molecular biological techniques in the last two decades has allowed the study of genetic factors in inflammatory bowel disease (IBD). A variety of techniques have been employed to elucidate the effects of genes, starting with the clinical observations that IBD is more common in the relatives of patients than the general population, and the consistency of clinical features within families. The situation is likely to be much more complicated than single gene disorders, and it is estimated that between 10 and 20 genes may be involved. Genome scanning techniques using microsatellite markers have been employed to highlight areas of chromosomes linked to disease such as those on chromosomes 12 and 16. In addition association studies of specific genes such as HLA and cytokine genes have been carried out on functional or positional grounds. It is likely that a combination of these techniques will be required to elucidate the role of individual genes. Recently much work has been focused on genes that may determine clinical phenotype such as disease extent or severity or the response to treatment. Identification of these genes may lead to better targeting of therapy and prognostication, and they are likely to be easier to identify than disease susceptibility genes.