Autoimmune Diseases. Autoimmune diseases can affect almost any part of the body, including the heart, brain, nerves, muscles, skin, eyes, joints, lungs, kidneys, glands, the digestive tract, and blood vessels. The classic sign of an autoimmune disease is inflammation, which can cause redness, heat, pain, and swelling.n autoimmune disease of the thyroid gland that results in the overproduction of thyroid hormone. This causes such symptoms as nervousness, heat intolerance, heart palpitations, and unexplained weight loss. Immune system.