Hypomorphic defects of V(D)J recombination in humans lead to residual T cell development. In these lymphopenic conditions, homeostatic lymphocyte proliferation occurs, and key mechanisms that normally maintain host tolerance are altered, allowing peripheral expansion of oligoclonal and autoreactive T cells. Recently described murine models support this notion. This review describes human and murine situations, in which genetically determined T and B cell lymphopenia is associated with autoimmune manifestations.