Purpose of review Chronic allograft rejection is the endpoint of a myriad of complex mechanisms, culminating in graft destruction. A clear role for alloimmunity in the pathogenesis of the rejection response has been documented in many studies. However, recent studies demonstrate that the alloimmune response may be associated with autoimmunity. Moreover, these studies suggest that immune responses to autoantigens may trigger or exacerbate rejection. The purpose of this review is to evaluate recent studies on autoimmunity and alloimmunity as they could relate to allograft rejection and tolerance to organ allografts. Recent findings This review will highlight three areas as they relate to allo- and autoimmunity in transplantation: (1) specific autoantigens in the rejection response, (2) the role of regulatory T cells and (3) epitope spreading and molecular mimicry. Summary Recent studies reported in this review highlight the need for additional research into mechanisms for controlling autoimmunity that may identify therapeutic interventions to down-regulate alloimmunity and allograft rejection.