To try to understand autoimmunity, attention has often fallen on the process of cell death. After all, apoptosis is used during selection of immunocytes, cells in the target organs end up dying and mutations to cell death genes have been found in some autoimmune diseases. Furthermore, some autoimmune-prone mice fail to develop disease when certain cell death genes are deleted, and transgenic mice expressing other cell death genes develop autoimmunity. However, only a tiny proportion of human autoimmune disease is associated with mutations to individual genes and even in these rare cases the genetic background has a major influence on the severity of disease. An understanding of the pathophysiology of common autoimmune diseases will require elucidation of many different systems that interact in complex ways, of which the process of apoptosis is just one.