Allograft rejection is a major barrier to transplantation. To prevent allograft rejection, transplant recipients require long-term immunosuppression, which is associated with increased susceptibility to infection, increased risk of malignancy, and increased morbidity and mortality. A major goal in transplantation, therefore, is the induction of tolerance, to enable indefinite allograft survival without the need for life-long immunosuppression. This focus issue on tolerance in transplantation contains six Reviews written by experts in the field of tolerance, describing tolerance mechanisms, how these mechanisms can be studied to assess prognosis, and how they can be harnessed to induce tolerance.