The environmental factors that may influence susceptibilty to autoimmune disease form an important part of biomedical research.

Experts have established that an inverse relationship exists between the prevalence of autoimmune disease and that of infectious diseases. In regions where infectious disease is endemic, the incidence of autoimmune disease is typically low and to some degree, the reverse of this is also true. Some researchers attribute this to the lack of exposure to infectious agents in childhood, a concept known of as the hygiene hypothesis. This theory proposes that a lack of exposure to microorganisms and parasites suppresses normal development of the immune system and therefore increases susceptibility to allergic diseases. More specifically, the lack of exposure is believed to cause defects in how immune tolerance is established.
 

While some claim the hygiene hypothesis to be spurious, studies have shown that parasitic infection is associated with a reduction in the activity of autoimmune processes. One suggested mechanism is that the parasite supresses the host’s immune response as a means of self protection and that this happens to also provide a benefit to the host if they have an autoimmune disease. Ways in which the parasite is thought to attenuate the immune response may include disruption of the host’s cell signalling mechanisms and the production of ant-inflammatory substances.

By contrast, research has also shown a positive correlation between microbial infection and autoimmune disease. Infection with the bacteria Klebsiella pneumoniae has been associated with the condition ankylosing spondylitis and coxsackievirus B infection has been linked to type 1 diabetes. These infective agents are thought to secrete super antigens that activate B-lymphocytes, which develop into plasma cells and produce a range of antibodies, some of which may target self-antigens.

Certain chemicals are known to be associated with the development of autoimmune diseases. One well know example of such a disease is drug-induced lupus erythematosus. Cigarette smoking is now known to be a significant risk factor for the development of rheumatoid arthritis.