In the article recent advances in the etiology of inflammatory bowel disease, which remain unknown despite intensive research effort, are presented. The role of the mucosal immune system in the mechanismus of inflammatory bowel disease, have been proven although the effector mechanism as well as target cells have not been precisely identified. In the past decade, research was directed particularly toward immunology, genetics and infectology. Numerous microbes are mentioned as possible agents, most frequently Mycobacterium paratuberculosis, measles virus and Listeria monocytogenes. All these studies may have a significant impact on diagnosis and treatment of classical forms of chronic intestinal diseases and their variants.