Diseases Home. There are more than 80 types of autoimmune diseases, which are also known as autoimmune disorders. Autoimmune diseases can affect almost any organ or body system. In many people with autoimmune disease, the first symptoms are fatigue, muscle aches, and low fever.ypes of autoimmune diseases that affect the digestive tract (including the mouth) are: 1  Autoimmune hepatitis. 2  Behcet'behçet s. 3  Disease'crohn s. 4  Disease primary biliary. 5  Cirrhosis. 6  Scleroderma ulcerative. 7  Colitis celiac.  disease