Autoimmune diseases are caused by the immune system mistakenly attacking something normally found inside the body. This misplaced assault causes localized inflammation in the areas of the body where the attack occurs and may also cause symptoms throughout the body. The nature of each autoimmune disease depends on the body protein that triggers the immune system to mistakenly react.  For some autoimmune diseases, the identity of this trigger is known, while for others the trigger is suspected but researchers have yet to confirm it.

Despite uncovering the trigger for several autoimmune diseases, researchers do not yet know why the immune system begins to attack normal body proteins in the first place. However, there are several theories as to what might make the immune system mistakenly attack normal body molecules. One idea is that infection with some kind of virus that has molecular similarity with some normal body molecule may prime the immune system to attack its own molecules later on. Many autoimmune diseases appear to run in families, suggesting that genetics or shared environment may also play a role.