The search for the susceptibility alleles for the complex genetic conditions of type 1 diabetes and autoimmune thyroid diseases has gained momentum in recent years. Studies have revealed several novel disease susceptibility alleles of relevance to both conditions, which brings the total number of genetic variants contributing to type 1 diabetes to ten. Additional genetic loci remain to be discovered, particularly in the autoimmune thyroid diseases. In the future, the density and coverage of single nucleotide polymorphisms available for high throughput genotyping will improve, and detailed analysis of the role of copy number variants in these diseases will shed new light on the pathogenesis of these common endocrinopathies.