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The immune system protects the body from potentially harmful substances (antigens) such as microorganisms, toxins, cancer cells, and foreign blood or tissues from another person or species. Antigens are destroyed by the immune response, which includes production of antibodies (molecules that attach to the antigen and make it more susceptible to destruction) and sensitized lymphocytes (specialized white blood cells that recognize and destroy particular antigens).

Immune system disorders occur when the immune response is inappropriate, excessive, or lacking. Autoimmune disorders develop when the immune system destroys normal body tissues. This is caused by a hypersensitivity reaction similar to allergies, where the immune system reacts to a substance that it normally would ignore. In allergies, the immune system reacts to an external substance that would normally be harmless. With autoimmune disorders, the immune system reacts to normal "self" body tissues.

Normally, the immune system is capable of differentiating "self" from "non-self" tissue. Some immune system cells (lymphocytes) become sensitized against "self" tissue cells, but these cells are usually controlled (suppressed) by other lymphocytes. Autoimmune disorders occur when the normal control process is disrupted. They may also occur if normal body tissue is altered so that it is no longer recognized as "self." The mechanisms that cause disrupted control or tissue changes are not known. One theory holds that various microorganisms and drugs may trigger some of these changes, particularly in people with a genetic predisposition to an autoimmune disorder.

Autoimmune disorders result in destruction of one or more types of body tissues, abnormal growth of an organ, or changes in organ function. The disorder may affect only one organ or tissue type or may affect multiple organs and tissues. Organs and tissues commonly affected by autoimmune disorders include blood components such as red blood cells, blood vessels, connective tissues, endocrine glands such as the thyroid or pancreas, muscles, joints, and skin.

A person may experience more than one autoimmune disorder at the same time. Examples of autoimmune (or autoimmune-related) disorders include: