A person's sex also seems to have some role in the development of autoimmunity; that is, most autoimmune diseases are "sex-related". Nearly 75% of the more than 23.5 million Americans who suffer from autoimmune disease are women, although it is less-frequently acknowledged that millions of men also suffer from these diseases. According to the American Autoimmune Related Diseases Association (AARDA), autoimmune diseases that develop in men tend to be more severe. A few autoimmune diseases that men are just as or more likely to develop as women include: ankylosing spondylitis, type 1 diabetes mellitus, granulomatosis with polyangiitis, Crohn's disease, Primary sclerosing cholangitis and psoriasis.

The reasons for the sex role in autoimmunity vary. Women appear to generally mount larger inflammatory responses than men when their immune systems are triggered, increasing the risk of autoimmunity. Involvement of sex steroids is indicated by that many autoimmune diseases tend to fluctuate in accordance with hormonal changes, for example: during pregnancy, in the menstrual cycle, or when using oral contraception. A history of pregnancy also appears to leave a persistent increased risk for autoimmune disease. It has been suggested that the slight, direct exchange of cells between mothers and their children during pregnancy may induce autoimmunity. This would tip the gender balance in the direction of the female.

Another theory suggests the female high tendency to get autoimmunity is due to an imbalanced X chromosome inactivation. The X-inactivation skew theory, proposed by Princeton University's Jeff Stewart, has recently been confirmed experimentally in scleroderma and autoimmune thyroiditis. Other complex X-linked genetic susceptibility mechanisms are proposed and under investigation.

An interesting inverse relationship exists between infectious diseases and autoimmune diseases. In areas where multiple infectious diseases are endemic, autoimmune diseases are quite rarely seen. The reverse, to some extent, seems to hold true. The hygiene hypothesis attributes these correlations to the immune manipulating strategies of pathogens. While such an observation has been variously termed as spurious and ineffective, according to some studies, parasite infection is associated with reduced activity of autoimmune disease.

The putative mechanism is that the parasite attenuates the host immune response in order to protect itself. This may provide a serendipitous benefit to a host that also suffers from autoimmune disease. The details of parasite immune modulation are not yet known, but may include secretion of anti-inflammatory agents or interference with the host immune signaling.

A paradoxical observation has been the strong association of certain microbial organisms with autoimmune diseases.

For example, "Klebsiella pneumoniae" and coxsackievirus B have been strongly correlated with ankylosing spondylitis and diabetes mellitus type 1, respectively. This has been explained by the tendency of the infecting organism to produce super-antigens that are capable of polyclonal activation of B-lymphocytes, and production of large amounts of antibodies of varying specificities, some of which may be self-reactive (see below).

Certain chemical agents and drugs can also be associated with the genesis of autoimmune conditions, or conditions that simulate autoimmune diseases. The most striking of these is the drug-induced lupus erythematosus. Usually, withdrawal of the offending drug cures the symptoms in a patient.

Cigarette smoking is now established as a major risk factor for both incidence and severity of rheumatoid arthritis. This may relate to abnormal citrullination of proteins, since the effects of smoking correlate with the presence of antibodies to citrullinated peptides.

Kikuchi-Fujimoto disease (KFD) is a rare, self-limiting disorder that typically affects the cervical lymph nodes. Recognition of this condition is crucial, especially because it can easily be mistaken for tuberculosis, lymphoma, or even adenocarcinoma. Awareness of this disorder helps prevent misdiagnosis and inappropriate treatment.

Kikuchi's disease is a very rare disease mainly seen in Japan. Isolated cases are reported in North America, Europe, and Asia. It is mainly a disease of young adults (20–30 years), with a slight bias towards females. The cause of this disease is not known, although infectious and autoimmune causes have been proposed. The course of the disease is generally benign and self-limiting. Lymph node enlargmeent usually resolves over several weeks to six months. Recurrence rate is about 3%. Death from Kikuchi disease is extremely rare and usually occurs due to liver, respiratory, or heart failure.

Neuropsychiatric systemic lupus erythematosus or NPSLE refers to the neurological and psychiatric manifestations of systemic lupus erythematosus. SLE is a disease in which the immune system attacks the body's own cells and tissues. It can affect various organs or systems of the body. It is estimated that over half of people with SLE have neuropsychiatric involvement.

Some studies have suggested a genetic predisposition to the proposed autoimmune response. Several infectious candidates have been associated with Kikuchi disease.

Many theories exist about the cause of KFD. Microbial/viral or autoimmune causes have been suggested. "Mycobacterium szulgai" and "Yersinia" and "Toxoplasma" species have been implicated. More recently, growing evidence suggests a role for Epstein-Barr virus, as well as other viruses (HHV6, HHV8, parvovirus B19, HIV and HTLV-1) in the pathogenesis of KFD. However, many independent studies have failed to identify the presence of these infectious agents in cases of Kikuchi lymphadenopathy. In addition, serologic tests including antibodies to a host of viruses have consistently proven noncontributory and no viral particles have been identified ultrastructurally.

KFD is now proposed to be a nonspecific hyperimmune reaction to a variety of infectious, chemical, physical, and neoplastic agents. Other autoimmune conditions and manifestations such as antiphospholipid syndrome, polymyositis, systemic juvenile idiopathic arthritis, bilateral uveitis, arthritis and cutaneous necrotizing vasculitis have been linked to KFD. KFD may represent an exuberant T-cell-mediated immune response in a genetically susceptible individual to a variety of nonspecific stimuli.

Human leukocyte antigen class II genes are more frequent in patients with Kikuchi disease, suggesting a genetic predisposition to the proposed autoimmune response.

Management of neuropsychiatric lupus is similar to the management of neuropsychiatric disease in patients without lupus. Treatment depends on the underlying causes of a patient’s disease, and may include immunosuppressants, anticoagulants, and symptomatic therapy.

CNS demyelinating autoimmune diseases are autoimmune diseases which primarily affect the central nervous system.

Examples include:

- Diffuse cerebral sclerosis of Schilder

- Acute disseminated encephalomyelitis

- Acute hemorrhagic leukoencephalitis

- Multiple sclerosis (though the cause is unknown, it is sure that immune system is involved)

- Transverse myelitis

- Neuromyelitis optica

The number of new cases a year is unknown. According to the California Encephalitis Project, the disease has a higher incidence than its individual viral counterparts in patients younger than 30. The largest case series to date characterized 577 patients with anti-NMDA receptor encephalitis. The epidemiological data were limited, but this study provides the best approximation of disease distribution. It found that women are disproportionally affected, with 81% of cases reported in female patients. Disease onset is skewed toward children, with a median age of diagnosis of 21 years. Over a third of cases were children, while only 5% of cases were patients over the age of 45. This same review found that 394 out of 501 patients (79%) had a good outcome by 24 months. 30 patients (6%) died, and the rest were left with mild to severe deficits. The study also confirmed that patients with the condition are more likely to be of Asian or African origin.

Given that some conditions as MS show cortical damage together with the WM damage, there has been interest if this can appear as a secondary damage of the WM. It seems that some researchers claim so.

Many individuals have mild symptoms, which recur infrequently, while others may have persistent problems that become debilitating or life-threatening.

Many health conditions can cause autonomic neuropathy. Some common causes of autonomic neuropathy include:

- Diabetes, which is the most common cause of autonomic neuropathy, can gradually cause nerve damage throughout the body.

- Injury to nerves caused by surgery or radiation to the neck.

- Treatment with certain medications, including some drugs used in cancer chemotherapy.

- Abnormal protein buildup in organs (amyloidosis), which affects the organs and the nervous system.

- Other chronic illnesses, such as Parkinson's disease, multiple sclerosis and some types of dementia.

- Autonomic neuropathy may also be caused by an abnormal attack by the immune system that occurs as a result of some cancers (paraneoplastic syndrome).

- Certain infectious diseases. Some viruses and bacteria, such as botulism, Lyme disease and HIV, can cause autonomic neuropathy.

- Inherited disorders. Certain hereditary disorders can cause autonomic neuropathy.

- Autoimmune diseases, in which the immune system attacks and damages parts of the body, including the nerves. Examples include Sjogren's syndrome, systemic lupus erythematosus, rheumatoid arthritis and celiac disease. Guillain-Barre syndrome is an autoimmune disease that happens rapidly and can affect autonomic nerves.

Relapsing polychondritis is an autoimmune disease in which the body's immune system begins to attack and destroy the cartilage tissues in the body. It has been postulated that both cell-mediated immunity and humoral immunity are responsible.

Reasons for disease onset are not known, but there is no evidence of a genetic predisposition to developing relapsing polychondritis. However, there are cases where multiple members of the same family have been diagnosed with this illness. Studies indicate that some genetic contribution to susceptibility is likely.

Nervous system disease refers to a small class of medical conditions affecting the nervous system.

The Nervous System Diseases can be divided into two categories:

- Central nervous system disease in the CNS

- Peripheral neuropathy in the PNS

Recently it has been found that CSF from MS patients can carry the disease to rodents, opening the door to an alternative model.

The clinical features and course of the condition, the associated auto-antibodies against relevant antigens, and the response to treatment, all suggest that Bickerstaff brainstem encephalitis is an autoimmune disease. However, each of these criteria fails to fit a substantial proportion of patients, and there is no single test or feature which is diagnostic of Bickerstaff brainstem encephalitis. It is therefore possible that a proportion of cases are due to other causes, such as infection or lymphoma, but remain undiagnosed. It is also possible that there is more than one autoimmune disease that can cause an illness which would currently be diagnosed as Bickerstaff's. There is certainly overlap between Guillain–Barré syndrome, Miller Fisher syndrome and Bickerstaff brainstem encephalitis, as well as other conditions associated with anti-ganglioside antibodies such as chronic ophthalmoplegia with anti-GQ1b antibody.

and the pharyngo-cervico-brachial variant of GBS.

Prognosis is poor, however, current analysis suggests that those associated with thymoma, benign or malignant, show a less favorable prognosis (CASPR2 Ab positive).

Bickerstaff brainstem encephalitis is a rare inflammatory disorder of the central nervous system, first described by Edwin Bickerstaff in 1951. It may also affect the peripheral nervous system, and has features in common with both Miller Fisher syndrome and Guillain–Barré syndrome.

Incidence of demyelinating diseases vary from disorder to disorder. Some conditions, such as Tabes dorsalis appear predominantly in males and begins in mid-life. Optic neuritis on the other hand, occurs preferentially in females typically between the ages of 30 and 35. Other conditions such as multiple sclerosis vary in prevalence depending on the country and population. This condition can appear in children as well as adults.

Lupus systemic erythematosus is one of the most common causes of cerebritis as it is believed that more than half of the patients with lupus from the United States suffer from a degree or another of lupus cerebritis.

The exact pathophysiological process of lupus cerebritis is unknown. The proposed mechanisms are likely due to the assault of several autoimmune system changes, including the following:

- Circulating immune complexes. The immune complexes, which consist of DNA and anti-DNA, cause an inflammatory response as well as a disruption of the blood–brain barrier. These circulating complexes have been found trapped in the highly vascular choroid plexus of SLE patients upon autopsy. True vasculitis, however, is found only in about 10% of patients with cerebral lupus.

- Anti-neuronal antibodies. The three identified anti-neuronal antibodies postulated in CNS involvement are the lympho-cytotoxic antibodies (LCAs), which somehow react with brain tissue and interfere with the neuron's ability to respond. LCAs have a specific role and are found in both the serum and cerebrospinal fluid (CSF) of lupus patients with cerebritis. These antibodies also correlate with cognitive and visual spatial defects. Second, the anti-neuronal membrane antibodies are targeted directly to neuronal antigens. They, too, are found in the serum of SLE patients with cerebritis. And third, the intracytoplasmic antibodies target the constituents of the neuron cells and they are found in the CSF and serum. These antibodies are seen in 90% of SLE patients with psychosis.

- Antiphospholipid antibodies. The two antibodies implicated are anticardiolipin and lupus anticoagulant. Anticardiolipin antibodies attach to the endothelial lining of cells, causing endothelial damage, platelet aggregation, inflammation, and fibrosis.

- Cytokine release. The final mechanism of lupus cerebritis involves the cytokines. The cytokines trigger edema, endothelial thickening, and infiltration of neutrophils in brain tissue. Two cytokines, interferon alpha and interleukin-6, have been found in the CSF of SLE patients with psychosis.

However, it is not clear which mechanism is the actual cause of cerebritis in lupus patients. Specialists believe that all mechanisms may be present at the same time or they may act independently.

In very rare cases, cerebritis may occur as a result of a Klebsiella pneumoniae infection.

One other reason to develop cerebritis is an infection caused by bacteria, viruses, or other organisms. Infections can occur when infectious agents enter the brain through the sinuses or as a result of trauma. Some pathogens are also capable of passing over the blood–brain barrier and entering the brain through the bloodstream, despite the fact that the body has evolved defenses which are specifically designed to prevent this.

The role of prolonged cortical myelination in human evolution has been implicated as a contributing factor in some cases of demyelinating disease. Unlike other primates, humans exhibit a unique pattern of postpubertal myelination, which may contribute to the development of psychiatric disorders and neurodegenerative diseases that present in early adulthood and beyond. The extended period of cortical myelination in humans may allow greater opportunity for disruption in myelination, resulting in the onset of demyelinating disease. Furthermore, it has been noted that humans have significantly greater prefrontal white matter volume than other primate species, which implies greater myelin density. Increased myelin density in humans as a result of a prolonged myelination may therefore structure risk for myelin degeneration and dysfunction. Evolutionary considerations for the role of prolonged cortical myelination as a risk factor for demyelinating disease are particularly pertinent given that genetics and autoimmune deficiency hypotheses fail to explain many cases of demyelinating disease. As has been argued, diseases such as multiple sclerosis cannot be accounted for by autoimmune deficiency alone, but strongly imply the influence of flawed developmental processes in disease pathogenesis. Therefore, the role of the human-specific prolonged period of cortical myelination is an important evolutionary consideration in the pathogenesis of demyelinating disease.

"N"-Methyl D-aspartate receptor (NMDAR) Ab encephalitis is the most common Ab-mediated autoimmune encephalopathy. It was first described in 2005 as a paraneoplastic syndrome associated with ovarian teratomas in young women and the antigenic target was determined in 2007, associated with antibodies against NR1 or NR2 subunits of the NMDA receptor. Irani et al. in 2010 presented NMDAR Ab encephalitis in a predominantly non-paraneoplastic disorder of both sexes.

The mechanism for paraneoplastic syndrome varies from case to case. However, pathophysiological outcomes usually arise from when a tumor arises. Paraneoplastic syndrome often occurs alongside associated cancers as a result of activated immune systems. In this scenario, the body may produce antibodies to fight off the tumor by directly binding and destroying the tumor cell. Paraneoplastic disorders may arise in that antibodies would cross-react with normal tissues and destroy them.

The recovery process from anti-NMDA encephalitis can take many months. The symptoms reappear in reverse order: The patient may begin to experience psychosis again, leading many people to falsely believe the patient is not recovering. As the recovery process continues on, the psychosis fades. Lastly, the person's social behavior and executive functions begin to improve.

Over 40 laboratory tests were initially conducted to rule out various pathogens and environmental toxins. These tests were used to try to identify potential viruses carried by humans, pigs, or both, including rotoviruses, adenoviruses, hepatitis A, and hepatitis E. They also tried to identify bacteria such as salmonella and escherichia coli (e. coli), and parasites such as Giardia and cryptosporidium that could be causing the symptoms. All were ruled out.

Neurodegenerative diseases were considered specifically because of the similarity of symptoms and animal involvement thus included investigation of prion associated diseases such as bovine spongiform encephalopathy (BSE), chronic wasting disease (CWD), and variant Creutzfeldt–Jakob disease (vCJD). These all have highly transmissible pathogenic agents that induce brain damage. Since no pathogenic agent had been found, these diseases were ruled out as being related.

Next two very similar neuropathies were ruled out. Guillain–Barré syndrome (GBS) induces an acute autoimmune response which affects the Schwann cells in the peripheral nervous system. GBS is usually triggered by an infection that causes weakness and tingling that may lead to muscle loss. This condition may be life-threatening if muscle atrophy ascends to affect the pulmonary or cardiac systems. So far, no infectious agents have been found that relate to the current disease, progressive infammatory neuropathy. They looked at chronic inflammatory demyelinating polyneuropathy (CIDP) which is characterized by progressive weakness and sensory impairment in the arms and legs. Damage occurs to the myelin sheath in the peripheral nervous system. As doctors at the Mayo Clinic were beginning to note, the problem they were seeing in progressive inflammatory neuropathy was occurring in the spinal nerve roots.

Conditions associated with myelitis include:

- Acute disseminated encephalomyelitis: autoimmune demyelination of the brain causing severe neurological signs and symptoms

- Multiple sclerosis: demyelination of the brain and spinal cord

- Neuromyelitis optica or Devic's disease: immune attack on optic nerve and spinal cord

- Sjögren's syndrome: destruction of the exocrine system of the body

- Systemic lupus erythematosus: a systemic autoimmune disease featuring a wide variety of neurological signs and symptoms

- Sarcoidosis: chronic inflammatory cells form as nodules in multiple organs

- Atopy: an immune disorder of children manifesting as eczema or other allergic conditions. It can include atopic myelitis, which causes weakness.