A healthy mucosal immune system prevents numerous diseases whether they are caused by pathogens or faulty tolerance to non-pathogenic antigens. Some methods for assessing immune responses have not changed for decades but have been applied in conjunction with new strategies. New methods have been developed recently that improve on existing mouse models and allow for assessment of cellular and molecular pathways that are involved in mucosal immune responses. Reviewed here are components of the mucosal immune system with attention paid to the gut-associated lymphoid tissue and some of the new methods for assessing immune responses.