Different autoimmune diseases affect different tissues, and they are caused by different underlying immune system defects. For example, in multiple sclerosis, the myelin sheaths that insulate nerves are damaged. Lupus may affect many different tissues, including the joints and skin. Rheumatoid arthritis results in swollen, stiff and painful joints, particularly in the hands and wrists. And in scleroderma, the skin is primarily affected, although the blood vessels, muscles and internal organs may also be damaged.