The cause of autoimmune disease is unknown. There are many theories about what triggers autoimmune diseases, including: 1  bacteria or virus. 2  drugs. 3  chemical irritants. 4  environmental irritants.he following are some of the more common autoimmune diseases: 1  rheumatoid arthritis: inflammation of joints and surrounding tissues. 2  systemic lupus erythematosus: affects skin, joints, kidneys, brain, and other organs.