Cytokines mediate immune responses and are detectable in the normal gastrointestinal mucosa. It is unclear how cytokines are physiologically regulated but in inflammatory enteropathies their expression is often greatly increased and may account for the tissue damage observed. T-cells may be sub-divided according to the pattern of cytokines which they secrete. TH1 cytokine expression is increased in delayed type IV cell mediate immune responses whereas TH2 cytokines are raised in diseases in which humoral mechanisms are more important. Cytokines are secreted by macrophages in relatively greater amounts than from T-cells. They are non-specific products of inflammation and may account for the majority of tissue damage seen in mucosal disease. The pattern of cytokine secretion may determine the immunopathogenesis of an inflammatory disorder. The ultimate goal of cytokine research is the development of therapeutic measures based on a better understanding of their actions which may be achieved with a better understanding of the molecular immune-microenvironment in inflammatory enteropathies. Studies with transgenic mice and gene targeted mice have important implications to the understanding of the immune system and its role in intestinal diseases.