Recent advances in islet transplantation have enabled physicians to cure type 1 autoimmune diabetes, but at the cost of lifelong immunosuppression with its attendant side effects and long-term health risks. To eliminate the need for immunosuppression, researchers have developed methods for inducing tolerance to transplanted allografts. Tolerance-based transplantation using costimulation blockade has proven remarkably successful in many animal model systems. The most widely used animal model system for studying islet transplantation in type 1-like autoimmune diabetes is the NOD mouse. Unfortunately, this strain has proven resistant to costimulation blockade-based transplantation tolerance protocols that are successful in chemically diabetic mice given islet grafts. It has been assumed that resistance to transplantation tolerance in the NOD mouse is (1) related to autoimmunity directed against its pancreatic beta cells, (2) a consequence of that autoimmunity, and (3) under the control of the same genes that control autoimmunity. In this review, we provide arguments to challenge these assumptions. We describe a new animal model and a new conceptual framework based on data indicating that the mechanisms responsible for resistance to transplantation tolerance and beta cell autoimmunity are not identical. We believe that the recent discoveries we describe will have important implications for the development of tolerance-based transplantation therapies and their translation from the laboratory to the clinic.