The immune system has evolved to ensure protection against ever changing microbial pathogens. The potential of lymphocytes to recognize 'self' is controlled by a process called 'self tolerance'. Improved understanding of the mechanisms of immunological tolerance is key to understanding the pathogenesis of autoimmune disorders and cancers, and may lead to strategies to harness tolerance to replace the lifelong need for immunosuppressive drugs after organ transplantation. In this Review, Waldmann provides an overview of the mechanisms of self tolerance and assesses the prospects of translating this knowledge to patient care.