The most commonly encountered chronic enteropathies in dogs are inflammatory bowel disease (IBD), food allergies, and small intestinal bacterial overgrowth. Recent research in the field of immunopathogenesis of IBD and food allergy in human beings have made available new therapeutic options with immunomodulatory drugs. However, the mechanisms involved in the pathogenesis of canine IBD and food allergy have not been elucidated so far. Further studies focusing on the immunological dysregulation in the mucosa as well as clinical trials with new therapeutic modalities are needed to improve our knowledge and approach to these chronic diseases in dogs.