Normal individuals maintain tolerance to the endogenous bacterial flora residing within their alimentary tract, a phenomenon mediated by the gastrointestinal lymphoid tissue. Loss of this tolerance is a key factor in the development of chronic intestinal inflammation. Manifestations of such uncontrolled inflammation in humans include inflammatory bowel disease and celiac disease. Dogs may similarly be affected, and although the etiopathogenesis is likely similar, the lesions differ. This review includes discussion of the factors involved in breakdown of mucosal tolerance, the immunologic basis of canine enteropathies, and the use of novel immunotherapies for these diseases.