An autoimmune disease is an illness in which your immune system incorrectly attacks your body. The immune system normally protects against germs like bacteria and viruses. When it detects these foreign invaders, it sends an army of combat cells to attack them. Normally, the immune system can tell the difference between foreign cells and its own cells. In an autoimmune disease, the immune system confuses a part of your body, such as the joints or the skin, as foreign.