The symptoms vary depending on the organs, glands, or body system being attacked. For example, when Hashimoto’s antibodies attack your thyroid, you may be tired and gain weight as your thyroid slows down. Rheumatoid arthritis attacks the joints, causing pain, swelling, stiffness, and disfigurement of your joints. Multiple sclerosis can cause balance problems. Alopecia results in hair loss. Common to most autoimmune diseases, however, is inflammation, which can cause swelling and pain.