Autoimmunity is accepted as the cause of a wide range of disorders, and it is suspected to be responsible for many more. Autoimmune diseases are classified as either general, in which the autoimmune reaction takes place simultaneously in a number of tissues, or organ specific, in which the autoimmune reaction targets a single organ.

Autoimmune disorders include the following:

• Systemic lupus erythematosus. A general autoimmune disease in which antibodies attack a number of different tissues. The disease recurs periodically and is seen mainly in young and middle-aged women.
• Rheumatoid arthritis. Occurs when the immune system attacks and destroys the tissues that line bone joints and cartilage. The disease occurs throughout the body, although some joints may be more affected than others.
• Goodpasture's syndrome. Occurs when antibodies are deposited in the membranes of both the lung and kidneys, causing both inflammation of kidney glomerulus (glomerulonephritis) and lung bleeding. It is typically a disease of young males.
• Grave's disease. Caused by an antibody that binds to specific cells in the thyroid gland, causing them to make excessive amounts of thyroid hormone.
• Hashimoto's thyroiditis. Caused by an antibody that binds to cells in the thyroid gland. Unlike in Grave's disease, however, this antibody's action results in less thyroid hormone being made.
• Pemphigus vulgaris. A group of autoimmune disorders that affect the skin.
• Myasthenia gravis. A condition in which the immune system attacks a receptor on the surface of muscle cells, preventing the muscle from receiving nerve impulses and resulting in severe muscle weakness.
• Scleroderma. Also called CREST syndrome or progressive systemic sclerosis, scleroderma affects the connective tissue.
• Autoimmune hemolytic anemia. Occurs when the body produces antibodies that coat red blood cells.
• Autoimmune thrombocytopenic purpura. Disorder in which the immune system targets and destroys blood platelets.
• Polymyositis and Dermatomyositis. Immune disorders that affect the neuromuscular system.
• Pernicious anemia. Disorder in which the immune system attacks the lining of the stomach in such a way that the body cannot metabolize vitamin B12.
• Sjögren's syndrome. Occurs when the exocrine glands are attacked by the immune system, resulting in excessive dryness.
• Ankylosing spondylitis. Immune system induced degeneration of the joints and soft tissue of the spine.
• Vasculitis. A group of autoimmune disorders in which the immune system attacks and destroys blood vessels.
• Type I diabetes mellitus. May be caused by an antibody that attacks and destroys the islet cells of the pancreas, which produce insulin.
• Amyotrophic lateral schlerosis. Also called Lou Gehrig's disease. An immune disorder that causes the death of neurons which leads to progressive loss of muscular control.
• Guillain-Barre syndrome. Also called infectious polyneuritis. Often occurring after an infection or an immunization (specifically Swine flu), the disease affects the myelin sheath, which coats nerve cells. It causes progressive muscle weakness and paralysis.
• Multiple sclerosis. An autoimmune disorder that may involve a virus affects the central nervous system, causing loss of coordination and muscle control.

To further understand autoimmune disorders, it is helpful to understand the workings of the immune system. The purpose of the immune system is to defend the body against attack by infectious microbes (germs) and foreign objects. When the immune system attacks an invader, it is very specific—a particular immune system cell will only recognize and target one type of invader. To function properly, the immune system must not only develop this specialized knowledge of individual invaders, but it must also learn how to recognize and not destroy cells that belong to the body itself. Every cell carries protein markers on its surface that identifies it in one of two ways: what kind of cell it is (e.g. nerve cell, muscle cell, blood cell, etc.) and to whom that cell belongs. These markers are called major histocompatability complexes (MHCs). When functioning properly, cells of the immune system will not attack any other cell with markers identifying it as belonging to the body. Conversely, if the immune system cells do not recognize the cell as "self," they attach themselves to it and put out a signal that the body has been invaded, which in turn stimulates the production of substances such as antibodies that engulf and destroy the foreign particles. In case of autoimmune disorders, the immune system cannot distinguish between "self" cells and invader cells. As a result, the same destructive operation is carried out on the body's own cells that would normally be carried out on bacteria, viruses, and other such harmful entities.

The reasons why immune systems become dysfunctional in this way is not well understood. However, most researchers agree that a combination of genetic, environmental, and hormonal factors play into autoimmunity. Researchers also speculate that certain mechanisms may trigger autoimmunity. First, a substance that is normally restricted to one part of the body, and therefore not usually exposed to the immune system, is released into other areas where it is attacked. Second, the immune system may mistake a component of the body for a similar foreign component. Third, cells of the body may be altered in some way, either by drugs, infection, or some other environmental factor, so that they are no longer recognizable as "self" to the immune system. Fourth, the immune system itself may be damaged, such as by a genetic mutation, and therefore cannot function properly.

The symptoms of the above disorders include:

• Systemic lupus erythematosus. Symptoms include fever, chills, fatigue, weight loss, skin rashes (particularly the classic "butterfly" rash on the face), vasculitis, polyarthralgia, patchy hair loss, sores in the mouth or nose, lymph-node enlargement, gastric problems, and, in women, irregular periods. About half of those who suffer from lupus develop cardiopulmonary problems, and some may also develop urinary problems. Lupus can also effect the central nervous system, causing seizures, depression, and psychosis.
• Rheumatoid arthritis. Initially may be characterized by a low-grade fever, loss of appetite, weight loss, and a generalized pain in the joints. The joint pain then becomes more specific, usually beginning in the fingers, then spreading to other areas, such as the wrists, elbows, knees, and ankles. As the disease progresses, joint function diminishes sharply and deformities occur, particularly the characteristic "swan's neck" curling of the fingers.
• Goodpasture's syndrome. Symptoms are similar to that of iron deficiency anemia, including fatigue and pallor. Symptoms involving the lungs may range from a cough that produces bloody sputum to outright hemorrhaging. Symptoms involving the urinary system include blood in the urine and/or swelling.
• Grave's disease. This disease is characterized by an enlarged thyroid gland, weight loss without loss of appetite, sweating, heart palpitations, nervousness, and an inability to tolerate heat.
• Hashimoto's thyroiditis. This disorder generally displays no symptoms.
• Pemphigus vulgaris. This disease is characterized by blisters and deep lesions on the skin.
• Myasthenia gravis. Characterized by fatigue and muscle weakness that at first may be confined to certain muscle groups, but then may progress to the point of paralysis. Myasthenia gravis patients often have expressionless faces as well as difficulty chewing and swallowing. If the disease progresses to the respiratory system, artificial respiration may be required.
• Scleroderma. Disorder is usually preceded by Raynaud's phenomenon. Symptoms that follow include pain, swelling, and stiffness of the joints, and the skin takes on a tight, shiny appearance. The digestive system also becomes involved, resulting in weight loss, appetite loss, diarrhea, constipation, and distention of the abdomen. As the disease progresses, the heart, lungs, and kidneys become involved, and malignant hypertension causes death in approximately 30% of cases.
• Autoimmune hemolytic anemia. May be acute or chronic. Symptoms include fatigue and abdominal tenderness due to an enlarged spleen.
• Autoimmune thrombocytopenic purpura. Characterized by pinhead-size red dots on the skin, unexplained bruises, bleeding from the nose and gums, and blood in the stool.
• Polymyositis and Dermatomyositis. In polymyositis, symptoms include muscle weakness, particularly in the shoulders or pelvis, that prevents the patient from performing everyday activities. In dermatomyositis, the same muscle weakness is accompanied by a rash that appears on the upper body, arms, and fingertips. A rash may also appear on the eyelids, and the area around the eyes may become swollen.
• Pernicious anemia. Signs of pernicious anemia include weakness, sore tongue, bleeding gums, and tingling in the extremities. Because the disease causes a decrease in stomach acid, nausea, vomiting, loss of appetite, weight loss, diarrhea, and constipation are possible. Also, because Vitamin B12 is essential for the nervous system function, the deficiency of it brought on by the disease can result in a host of neurological problems, including weakness, lack of coordination, blurred vision, loss of fine motor skills, loss of the sense of taste, ringing in the ears, and loss of bladder control.
• Sjögren's syndrome. Characterized by excessive dryness of the mouth and eyes.
• Ankylosing spondylitis. Generally begins with lower back pain that progresses up the spine. The pain may eventually become crippling.
• Vasculitis. Symptoms depend upon the group of veins affected and can range greatly.
• Type I diabetes mellitus. Characterized by fatigue and an abnormally high level of glucose in the blood (hyperglycemia).
• Amyotrophic lateral schlerosis. First signs are stumbling and difficulty climbing stairs. Later, muscle cramps and twitching may be observed as well as weakness in the hands making fastening buttons or turning a key difficult. Speech may become slowed or slurred. There may also be difficluty swallowing. As respiratory muscles atrophy, there is increased danger of aspiration or lung infection.
• Guillain-Barre syndrome. Muscle weakness in the legs occurs first, then the arms and face. Paresthesias (a prickly, tingling sensation) is also felt. This disorder affects both sides of the body and may involve paralysis and the muscles that control breathing.
• Multiple sclerosis. Like Lou Gehrig's disease, the first symptom may be clumsiness. Weakness or exhaustion is often reported, as well as blurry or double vision. There may be dizziness, depression, loss of bladder control, and muscle weakness so severe that the patient is confined to a wheelchair.

A number of tests are involved in the diagnosis of autoimmune diseases, depending on the particular disease; e.g. blood tests, cerebrospinal fluid analysis, electromylogram (measures muscle function), and magnetic resonance imaging of the brain. Usually, these tests determine the location and extent of damage or involvement. They are useful in charting progress of the disease and as baselines for treatment.

The principle tool, however, for authenticating autoimmune disease is antibody testing. Such tests involve measuring the level of antibodies found in the blood and determining if they react with specific antigens that would give rise to an autoimmune reaction. An elevated amount of antibodies indicates that a humoral immune reaction is occurring. Since elevated antibody levels are also seen in common infections, they must be ruled out as the cause for the increased antibody levels.

Antibodies can also be typed by class. There are five classes of antibodies, and they can be separated in the laboratory. The class IgG is usually associated with autoimmune diseases. Unfortunately, IgG class antibodies are also the main class of antibody seen in normal immune responses.

The most useful antibody tests involve introducing the patient's antibodies to samples of his or her own tissue, usually thyroid, stomach, liver, and kidney tissue. If antibodies bind to the "self" tissue, it is diagnostic for an autoimmune disorder. Antibodies from a person without an autoimmune disorder would not react to "self" tissue.

Treatment of autoimmune diseases is specific to the disease, and usually concentrates on alleviating or preventing symptoms rather than correcting the underlying cause. For example, if a gland involved in an autoimmune reaction is not producing a hormone such as insulin, administration of that hormone is required. Administration of a hormone, however, will restore the function of the gland damaged by the autoimmune disease.

The other aspect of treatment is controlling the inflammatory and proliferative nature of the immune response. This is generally accomplished with two types of drugs. Steroid compounds are used to control inflammation. There are many different steroids, each having side effects. The proliferative nature of the immune response is controlled with immunosuppressive drugs. These drugs work by inhibiting the replication of cells and, therefore, also suppress non-immune cells leading to side effects such as anemia.

Systemic enzyme therapy is a new treatment that is showing results for rheumatoid arthritis, multiple sclerosis, ankylosing spondylitis, and other inflammatory diseases. Enzymes combinations of pancreatin, trypsin, chymotrypsin, bromelain, and papain help stimulate the body's own defenses, accelerate inflammation in order to reduce swelling and improve circulation, and break up the immune complexes within the bloodstream. Symptoms have been reduced using this treatment.

Other treatments that hold some promise are irradiation of the spleen and gene therapy. Splenic irradiation is touted to be a safe, alternative for patients with autoimmune blood diseases, especially autoimmune hemolytic anemia, or others with compromised immune systems, such as HIV patients and the elderly. It is reported to have few side effects and seems to be working. Cytokine and cytokine inhibitor genes injected directly into muscle tissue also appear to be effective in treating Type I diabetes mellitus, systemic lupus erythematosus, thyroditis, and arthritis.

Prognosis depends upon the pathology of each autoimmune disease.

Most autoimmune diseases cannot be prevented. Though the mechanisms involved in how these diseases affect the body are known, it is still unclear why the body turns on itself. Since more women than men seem to be affected by some of these disorders (e.g. lupus), some researchers are looking into hormones as a factor. This, and gene therapy, may be the preventatives of the future.