Autoimmunity and inheritance of complex characters behold an explosive interest in biology over the last 15 years. Research in the genetics of autoimmunity has been impelled by the isolation of genetic markers allowing tracing of heredity. The annotation and sequencing of the human and mouse genomes provide with the potential for further advancements, through the development of new technologies. This review aims to summarize advances made in the autoimmunity field, centered in type 1 diabetes in the NOD mouse model. It also aims to demonstrate that animal models, albeit some phenotypic and genetic dissimilarities with the human diseases, still remain the best way to move towards an understanding of the molecular mechanisms involved in autoimmunity. Assessing the current state of research in this field together with the increasing potential of novel biotechnology advancements, new insights to disease pathogenesis and discovery of molecular targets for intervention strategies are anticipated in the coming years.