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Autoimmune diseases are a broad group of disorders characterized by the involvement of adaptive immunity but also the innate immunity. Genetic defects underlying autoimmunity are rare, though increasingly described, and represent excellent opportunities to get insight into the function of specific molecules. In this sense, primary immunodeficiencys are perfect examples for increasing knowledge of how the immune system works. Although most of immunodeficiencies manifest mainly susceptibility to infections, autoimmunity is probably the second group of clinical signs. Both adaptive and innate immunodeficiencies are being broadly related with autoimmune disorders. This article reviews the main aspects regarding autoimmunity learned from immunodeficiencies; from dysregulation of classical humoral and cellular immunodeficiencies to dysregulation of innate immunodeficiencies, which are associated to auto inflammatory disorders.