Genome-scale analysis in type 1 diabetes has resulted in a number of non-major histocompatibility complex loci of varying levels of statistical significance. In no case has a specific gene been proven to be the source of genetic linkage at any candidate locus. Comparative analysis of the position of loci for type 1 diabetes with candidate loci from other autoimmune/inflammatory diseases shows considerable overlap. This supports a hypothesis that the underlying genetic susceptibility to type 1 diabetes may be shared with other clinically distinct autoimmune diseases such as systemic lupus erythemastosus, multiple sclerosis, and Crohn's Disease.