The intestinal mucosa constitutes an important barrier as it separates each individual from a large array of antigens within the bowel lumen. These luminal antigens may either be derived from pathogens or may be derived from harmless constituents such as ingested food or the normal intestinal flora. The dichotomy of potentially harmful and potentially harmless antigens encountered by the mucosal immune system poses the important task that, with regard to bacteria-derived antigens, the gut associated immune system is required to mount an efficient host defense against pathogenic bacteria but to maintain at the same time the regulatory control mechanisms which protect the human organism from hyperresponsiveness, and thus chronic inflammation, towards antigens from the normal intestinal flora. In the present review, we discuss variable host and bacterial factors which are likely to determine whether the immune response to pathogenic or normal intestinal bacteria will have beneficial or detrimental consequences for the human organism. Using infections with the prototype enteropathogens V. cholerae and enteropathogenic E. coli (ETEC), Y. enterocolitica induced reactive arthritis (ReA) and in more detail, inflammatory bowel diseases (IBD) as exemplary clinical situations, we review current hypotheses of how bacteria or their products are encountered by cellular components of the specific immune system and how this may relate to disease pathogenesis and the development of new treatment strategies.