By Dr Ananya Mandal, MD. There are several different types of autoimmune disease that may affect different organs and systems in the body. There are nearly 80 different types of autoimmune disorders. While some like Hashimoto’s thyroiditis are quite common, some are rarer. Scleroderma – this type of autoimmune disorder commonly affects the connective tissues of skin and blood vessels, muscles, and internal organs. 2  The disease usually affects women more commonly between ages 30 and 50 years. 3  Dermatomyositis – this condition results in inflammation of muscles and a skin rash.