Mucosal and systemic immune systems are quite separate in their properties and in the factors which regulate them. In man, assessment of immune status at gut level, including the capacity to respond to oral vaccines, should follow the general lines which are used in research and clinical investigation of systemic immunity. All of the currently available methods for direct studies of gut immunity have limitations, but a new technique, per-oral whole gut lavage with non-absorbable cleansing fluid, provides a system of gut perfusion. The value of this technique is illustrated by data on intestinal antibodies to bacterial LPS core antigens, of gut immunity in healthy African children, on the isotype of antibodies elicited by oral killed whole cell/cholera toxin B vaccine in coeliac disease patients, and on the effects of smoking on intestinal antibodies elicited by the oral typhoid vacine Ty21a in healthy UK adults. Finally, results of a recent comprehensive study show that immunological tests using faeces are likely to be highly misleading.