Behcet’s disease (BD) is an autoimmune and inflammatory disease that is mainly characterized by involvement of the gastrointestinal tract, cardiovascular system, genital tract and joints. The disease is more common in the Middle Eastern and Far Eastern countries and the frequency of recurrences and attacks varies among populations. Although the pathogenesis is not fully understood, there is evidence to suggest that immunodeficiency and specific patterns of production of immune regulatory mediators are important. Impaired autoimmune and inflammatory cells, target endothelial cells and prompt vasculitis in the involved organs. Elucidating the immunological mechanism of BD can facilitate the development of new therapies and therapeutic immunoregulatory interventions to prevent possible complications. New therapies, including manipulation of immune-regulating mediators such as interferon-alpha antagonists, have shown promising results in patients with BD. This review aims to consider the role of auto-inflammatory and autoimmune processes and related factors which give rise to the different manifestations of the disease in each involved organ.