Coeliac disease (gluten sensitive enteropathy) is a common, polygenic and multifactorial disorder that serves as a pioneering model for the study of inflammatory disease. A major environmental factor is known (ingested gluten from wheat), and there is unprecedented genetic and functional evidence pinpointing HLA-DQA1*05-DQB1*02 ( DQ2) and DQA1*03-DQB1*0302 ( DQ8) in disease predisposition. We discuss the current state of play in coeliac disease genetics, focussing particularly on the HLA complex. Emerging evidence suggests that additional HLA risk loci exert weak effects, independent of DQA1*05-DQB1*02, on the B8-DR3-DQ2 haplotype. There is also good evidence from linkage studies of disease gene(s) on chromosome 5q. We discuss the role and implications of linkage disequilibrium and haplotype blocks in complex disease gene mapping. We briefly address findings from studies of animal models for chronic inflammatory disease, and consider roles for both common genes associated with multiple inflammatory diseases, and genes unique to coeliac disease. The coeliac genetics research community has established a sound foundation for the identification of additional disease genes in the not-too-distant future. Functional studies will play a critical role, and coeliac disease has a promising future in this respect. Coeliac disease continues to function as a model disorder, facilitating the development and implementation of complex disease gene mapping strategies.