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.

Autoimmune diseases that affect multiple organ systems

• Systemic Lupus Erythematosus (SLE) – this is a chronic auto-inflammatory disease. It is seen more commonly among females. The diagnostic tests are usually positive for antibodies against nuclear proteins including nucleic DNA and RNA. Some of triggers for flare ups include UV radiation, viral infections and stress.
• Acquired Autoimmune Disorders caused by Human Immunodeficiency Virus (HIV) infection is also seen. Infection with HIV causes destruction of the immune system leading to damage to several organ systems and tissues.

Autoimmune diseases that affect the eyes

• Acute anterior uveitis – this is the commonest inflammatory disease of the iris of the eyes. There is a strong genetic association with HLA-B27.
• Sjögren's Syndrome – an autoimmune disease in which the immune system damages the glands that make moisture, such as tears and saliva.

Arthritis

• Ankylosing Spondylitis – this is a common form of chronic, inflammatory arthritis that is caused by autoimmune pathology. It affects the joints in the spine and the sacroiliac joints of the pelvis leading to severe pain, deformity and disability.
• Reactive Arthritis or Reiter's Syndrome – this is usually triggered by an infection. There are three classic symptoms of this condition including inflammatory arthritis of large joints (commonly knees and lower back), inflammation of the eyes with either  conjunctivitis or  uveitis and presence of urethritis in men (urethral inflammation) or cervicitis (cervical inflammation) in women.
• Rheumatoid arthritis – this is an autoimmune disorder affecting the tissues in the joints. It leads to severe damage of cartilage in the joints leading to inflammation. Other organs such as lungs, pericardium, pleura, and sclera of the eyes may also be affected.

Autoimmune diseases affecting hormone producing organs

• Diabetes Mellitus Type 1 – here the autoantibodies affect and target the insulin-producing beta cells of the pancreas leading to their severe deficiency. The lack of insulin leads to increased blood and urine glucose.
• Autoimmune Pancreatitis – this is an inflammatory condition that affects the pancreas.
• 21 - Hydroxylase Deficiency – this condition affects the adrenal glands. This condition leads to excess production of androgens, which are male sex hormones.
• Autoimmune Thyroiditis – this condition leads to inflammatory cells targeting cells of the thyroid causing them to be destroyed leading to an underactive thyroid gland. Chronic thyroiditis or Hashimoto's disease may being at any age are is often common among middle-aged women.
• Graves’ disease is an autoimmune disease of the thyroid gland that leads to an overactive thyroid gland.

Autoimmune diseases affecting the skin

• Scleroderma – this type of autoimmune disorder commonly affects the connective tissues of skin and blood vessels, muscles, and internal organs. The disease usually affects women more commonly between ages 30 and 50 years.
• Dermatomyositis – this condition results in inflammation of muscles and a skin rash. It may affect persons with cancers of the lungs, abdomen or other organs.
• Psoriasis – this is an autoimmune skin disease. There is excessive growth of the new cells underneath the layers of skin.
• Vitiligo – in this condition the cells that give pigment to the skin are destroyed leading to formation of white de-pigmented patches.
• Alopecia areata is seen when the immune system attacks hair follicles or the roots of the hair.

Autoimmune diseases affecting the nerves

• Multiple sclerosis – this is an autoimmune disease that affects the brain and the nerves. The autoimmune cells cause damage to the myelin sheath that normally acts as the protective covering that surrounds nerve cells.
• Myasthenia gravis – in this condition the immune system attacks the nerves and muscles leading to severe weakness

Autoimmune diseases affecting the blood and blood vessels

• Polyarteritis nodosa – this is a severe autoimmune disease affecting the small and medium-sized arteries that become inflamed and damaged. The risk of this condition rises with hepatitis b and C infections.
• Antiphospholipid antibody syndrome leading to damage to blood vessels
• Hemolytic anemia – this type of anemia is caused when the immunological cells damage the blood cells.
• Idiopathic thrombocytopenic purpura (ITP) – this causes damage to the blood platelets that are essential to formation of blood clots.

Autoimmune diseases affecting the gastrointestinal system

• Autoimmune Hepatitis – this type affects the liver when the body’s immune cells attack cells of the liver. There is a genetic predisposition to this condition. Autoimmune hepatitis affects 1-2 people per 100,000 per year and affects women much more often than men (70%). 
• Celiac disease – this is caused when the intestines react to foods containing gluten (e.g. wheat).
• Inflammatory bowel disease (IBD) – this condition leads to severe and chronic inflammation of the digestive tract. Crohn’s disease and ulcerative colitis are the commonest forms of IBD.
• Primary biliary cirrhosis – in this condition the immune system slowly destroys the liver’s bile ducts.