In the last few years, with the emergence of genome-wide association studies (GWAS), there has been an explosion of genetic discoveries for many complex genetic autoimmune diseases such as Crohn’s disease, type 1 diabetes, multiple sclerosis, and rheumatoid arthritis. Indeed, more genetic risk factors were identified for common diseases in 2007 than had been collectively reported before that year. Studies on juvenile idiopathic arthritis (JIA) are following in the footsteps of those studies, and the next few years look set to be exciting times in the search for JIA-susceptibility loci with large, well-powered international collaborative GWAS being performed. In this review, I will explain how the recent advances in genetic technologies, methodologies, and research in other autoimmune diseases has already led to a greater understanding of JIA genetic susceptibility. I will describe how this information can help not only in the understanding of JIA disease pathogenesis, but also in the classification of this heterogeneous disorder. Ultimately, genetics may also identify new disease pathways for therapeutic intervention, help predict outcome of disease, and additionally help predict response to treatment. Int J Adv Rheumatol 2010;8(1):8–15.