Hashimoto disease and Graves disease are two of the most common autoimmune disorders of the thyroid gland, the hormone-secreting organ (located in the throat near the larynx) that plays an important role in the development and maturation of all vertebrates. The thyroid is composed of closed sacs (follicles) lined with specialized thyroid cells. These cells secrete thyroglobulin, a large protein that acts as a storage molecule from which thyroid hormones are made and released into the blood. The rate at which this occurs is regulated by thyroid-stimulating hormone (TSH), which activates the thyroid cells by combining with TSH receptors found on the thyroid cell membrane. Hashimoto disease involves swelling of the gland (a condition called goiter) and a loss of thyroid hormone production (hypothyroidism). The autoimmune process underlying this disorder is thought to be instigated by helper T cells that react with thyroid antigens, although the mechanism is not completely understood. Once activated, the self-reactive T cells stimulate B cells to secrete antibodies against several target antigens, including thyroglobulin.

Graves disease is a type of overactive thyroid disease (hyperthyroidism) involving excess production and secretion of thyroid hormones. The disease arises with the development of antibodies that are directed against the TSH receptor on the thyroid cells and that can mimic the action of TSH. When bound to the receptor, the antibodies stimulate excessive secretion of thyroid hormones.

In both Hashimoto disease and Graves disease, the thyroid gland becomes infiltrated with lymphocytes and is partially destroyed. If the gland is completely destroyed, a condition called myxedema may ensue, involving a swelling of tissues, especially those around the face.

Autoimmune hemolytic anemia

A number of autoimmune disorders are grouped under the rubric autoimmune hemolytic anemia. All result from the formation of autoantibodies against red blood cells, an event that can lead to hemolysis (destruction of red blood cells). The autoantibodies sometimes appear after infection with the bacterium Mycoplasma pneumoniae, a rather uncommon cause of pneumonia. In that case the autoantibodies are directed against certain antigens that are present on red cells, and they are probably induced by a similar antigen in the microbes (an example of the cross-reaction of antigens). Autoantibodies directed against a different antigen of red blood cells are often produced in persons who have been taking the antihypertensive medication alpha methyldopa for several months; the reason for autoantibody development in such cases is unknown. Other drugs, such as quinine, sulfonamides, or even penicillin, very occasionally cause hemolytic anemia. In such cases it is thought that the drug acts as a hapten—that is, it becomes bound to a protein on the surface of red blood cells, and the complex becomes immunogenic.

The autoantibodies that form against red blood cells are categorized into two groups on the basis of their physical properties. Autoantibodies that bind optimally to red blood cells at 37 °C (98.6 °F) are categorized as warm-reacting. Warm-reacting autoantibodies belong primarily to the IgG class and cause about 80 percent of all cases of autoimmune hemolytic anemia. Autoantibodies that attach to red blood cells only when the temperature is below 37 °C are called cold-reacting. They belong primarily to the IgM class. Cold-reacting autoantibodies are efficient at activating the complement system and causing the cell to which they are bound to be destroyed. Nevertheless, as long as the body temperature remains at 37 °C, cold-reacting autoantibodies dissociate from the cell, and hemolysis is not severe. However, when limbs and skin are exposed to the cold for long periods of time, the temperature of circulating blood can be lowered, allowing cold-reacting autoantibodies to go to work. Infection with M. pneumoniae is met by cold-reacting antibodies.

Pernicious anemia and autoimmune gastritis

Pernicious anemia stems from a failure to absorb vitamin B₁₂ (cobalamin), which is necessary for the proper maturation of red blood cells. It is characteristically accompanied by a failure to secrete hydrochloric acid in the stomach (achlorhydria) and is in fact a symptom of severe autoimmune gastritis. To be absorbed by the small intestine, dietary vitamin B₁₂ must form a complex with intrinsic factor, a protein secreted by the parietal cells in the stomach lining. Pernicious anemia results when autoantibodies against intrinsic factor bind to it, preventing it from binding to vitamin B₁₂ and thus preventing the vitamin from being absorbed into the body. The autoantibodies also destroy the acid-secreting parietal cells, which leads to autoimmune gastritis.

Rheumatoid arthritis

Rheumatoid arthritis is a chronic inflammatory disease that affects connective tissues throughout the body, particularly the synovial membranes that line the peripheral joints. Rheumatoid arthritis is one of the most common autoimmune diseases. Its cause is not known, but a variety of altered immune mechanisms probably contribute to the disorder, especially in more severe cases.

One theory suggests that the inflammatory process of the disease is initiated by autoimmune reactions that involve one or more autoantibodies, referred to collectively as rheumatoid factor. The autoantibodies react with the tail region of the Y-shaped IgG molecule—in other words, rheumatoid factor is anti-IgG antibodies. Immune complexes form between rheumatoid factor and IgG and apparently are deposited in the synovial membrane of joints. The deposition triggers a type III hypersensitivity reaction, activating complement and attracting granulocytes, which causes inflammation and pain in the joints. The granulocytes release enzymes that break down cartilage and collagen in the joints, and this eventually can destroy the smooth joint surface that is needed for ease of movement. If immune complexes in the blood are not effectively removed by the liver and spleen, they can produce systemic effects similar to those precipitated by serum sickness.

The devastating effects of rheumatoid arthritis also have been seen in patients, especially younger ones, in whom no rheumatoid factor is detected, and thus other mechanisms of initiation of the disorder probably exist.