An autoimmune disease is a condition in which your immune system attacks your body. Common autoimmune diseases include type 1 diabetes, rheumatoid arthritis, and inflammatory bowel disease.Immune system disorders cause abnormally low activity or over activity of the immune system. In cases of immune system over activity, the body attacks and damages its own tissues (autoimmune diseases). Immune deficiency diseases decrease the body's ability to fight invaders, causing vulnerability to infections.