Chronic inflammatory diseases have been at the forefront of the new genome-wide association study era. Conditions such as coeliac disease, type 1 diabetes, Crohn's disease and ulcerative colitis have all benefited with multiple loci identified and replicated for each condition. As cohort sample numbers increase and researchers collaborate and share cohorts, common susceptibility loci are beginning to emerge between several diseases. Crohn's disease and coeliac disease both demonstrate considerable overlap in their common genetic susceptibility with other related conditions. These shared loci offer an insight into the biology of the conditions but still present researchers with the problem of attempting to identify the true causal variants.