Intestinal Behcet’s disease (Intestinal BD), one of the subtypes of Behcet’s disease (BD), leads the patients to poor prognosis. Typical finding is a deep oval ulcer locating at the ileo-cecal region, frequently perforating and forming fistulas with the other tissues or organs. Diagnostic criteria and therapeutic way for Intestinal BD have been discussed to improve the prognosis. In histological studies, the ulcer region is predominantly infiltrated by mononuclear cells and neutrophils, and expression of IFNγ, IL-12 and TNFα is observed. It is sometimes difficult to discriminate Intestinal BD from the inflammatory bowel diseases of Crohn’s disease (CD) and ulcerative colitis (UC) because of similar location and appearance of the ulceration among these diseases. Th1 and Th17 cells have been detected to be involved both in Intestinal BD and CD, whereas Th2 cells are associated with the pathophysiology of UC. Involvement of Peyer’s Patches is indicated both in Intestinal BD and CD, suggesting association of lymphatic tissue in gastrointestinal (GI) tracts with the two diseases. The difference between Intestinal BD and CD is distribution of the lesions, that is, most of the ulceration is located in the ileo-cecal region in Intestinal BD, whereas “skipped lesions” is found in almost entire GI tracts in CD. The pathogenesis of Intestinal BD, CD and UC, in particular, different mechanisms of immune dysregulation of the diseases, are discussed in this review