Discussions around the etiology of autoimmune disease routinely focus on the interplay between genes and the environment. In turn, efforts to ameliorate these diseases seek to modify genetic and environmental factors. However, there may be a third element that also accounts for the progression of autoimmunity. This article explores the role of chance, exemplified by the stochastic process of immune repertoire generation, in the evolution of autoimmunity. The presented modeling studies and concepts suggest that chance plays as significant a role as genes or environment. This hypothesis implies that a full understanding of the role of genes and environment will also require investigators to account for stochastic processes in building comprehensive disease models.