There are more than 80 different types of autoimmune diseases, but some of the most common ones are: 1  Graves' disease. 2  Hashimoto's thyroiditis. 3  Systemic lupus erythematosus (lupus). 4  Type 1 diabetes. 5  Multiple sclerosis (MS). 6  Rheumatoid arthritis.ommon Autoimmune Diseases. There are more than 80 different types of autoimmune diseases, but some of the most common ones are: 1  Graves' disease. 2  Graves’ disease is a type of autoimmunity in which the thyroid gland becomes overly active.