Although traditionally the adaptive immune system has been viewed as the essential contributor to autoimmune diseases, the evidence implicating the innate immune system has grown considerably in recent years. Several multisystem inflammatory diseases affect the uvea and occur as a result of a mutation in a gene coding for a component of the innate immune system. Diseases associated with uveitis such as ankylosing spondylitis, sarcoidosis, Behcet's disease and inflammatory bowel disease can best be conceptually understood by hypotheses that consider microbial infection and innate immunity as contributing factors.