The human gastrointestinal tract is colonized by an abundance of bacteria, which are in constant interaction with the epithelial lining usually leading to an intricate balance between tolerance and immunological response. There is ample evidence that the abundant presence of bacteria thus plays a role in the maintenance of human health, as well as in the induction of chronic inflammatory diseases of the gastrointestinal tract. Research in this field is, however, considerably hampered by the abundance of bacterial species, many of which have not even been characterized, and are difficult to culture specifically. These important limitations may to some extent be overcome by recent molecular biologic methods. Furthermore however, the adherent mucosal flora may differ largely from the luminal flora and that in excreta. These characteristics do not pertain to Helicobacter pylori, which generally colonizes the human stomach as a single strain with stable characteristics. Such colonization is stable throughout life, but can be treated. Furthermore, the association with chronic gastritis is very strong. For these reasons, H. pylori serves as an excellent model for the understanding of the processes involved in bacterial colonization and host response including mediation of immunoregulation, and the mechanisms by which this response can lead to disease.