AIED is generally caused by either antibodies or immune cells that cause damage to the inner ear. There are several theories that propose a cause of AIED:

- Bystander damage – Physical damage to the inner ear may lead to cytokine release that signals for an immune response. This may be a component of the "attack/remission cycle" of Meniere's disease.

- Cross-reactions – Accidental damage of the inner ear by antibodies or T-cells that recognize an inner ear antigen that is similar to a bacterial or viral antigen

- Genetic factors – Predisposition to developing an autoimmune disorder based on genes inherited

- Intolerance – The immune system may not be aware of all the antigens present in the inner ear until physical damage releases some of these antigens. As a result, the immune system treats these unfamiliar antigens as foreign and mounts an immune response.

Currently, the cross-reactions theory appears to be the favored mechanism of AIED pathogenesis.

Autoimmune inner ear disease (AIED) was first defined by Dr. Brian McCabe in a landmark paper describing an autoimmune loss of hearing. The disease results in progressive sensorineural hearing loss (SNHL) that acts bilaterally and asymmetrically, and sometimes affects an individual's vestibular system. AIED is used to describe any disorder in which the inner ear is damaged as a result of an autoimmune response. Some examples of autoimmune disorders that have presented with AIED are Cogan's syndrome, relapsing polychondritis, systemic lupus erythematosus, granulomatosis with polyangiitis, polyarteritis nodosa, Sjogren's syndrome, and Lyme disease.

Research has come to the consensus that AIED is the result of antibodies or other immune cells that cause damage to structures of the inner ear such as the cochlea and vestibular system. Of note, AIED is the only known SNHL that responds to medical treatment, but withholding treatment for longer than three months may result in permanent hearing loss and the need for cochlear implant installation.

Although AIED has been studied extensively over the past 25 years, no clear mechanism of pathogenesis has emerged. A recent paper performed a literature review of all relevant articles dating back to 1980, and proposed a mechanism of pathogenesis which includes an inflammatory response and immune cell attack on inner ear structures. This response leads to an over-activation of other immune cells such as T helper cells, resulting in vascular changes and cochlear harm. AIED appears to be a consequence of damaged sensorineural hearing due to electrochemical disturbances, microthrombosis, and immune cell deposition. Additionally, self-reactive antibodies and T-cells contribute to the aforementioned damage. Research has suggested a valuable next step in uncovering AIED pathogenesis is inquiry into the role of interleukin-1β (IL-1β).