The gastrointestinal tract is subjected to enormous and continual foreign antigenic stimuli from food and microbes. This organ must integrate complex interactions among diet, external pathogens, and local immunological and non-immunological processes. It is critical that protective immune responses are made to potential pathogens, while hypersensitivity reactions to dietary antigens are minimised. There is increasing evidence that fermentable dietary fibres and the newly described prebiotics can modulate various properties of the immune system, including those of the gut-associated lymphoid tissues (GALT). This paper reviews evidence for the immune-enhancing effects of dietary fibres. Changes in the intestinal microflora that occur with the consumption of prebiotic fibres may potentially mediate immune changes via: the direct contact of lactic acid bacteria or bacterial products (cell wall or cytoplasmic components) with immune cells in the intestine; the production of short-chain fatty acids from fibre fermentation; or by changes in mucin production. Although further work is needed to better define the changes, mechanisms for immunomodulation, and the ultimate impact on immune health, there is convincing preliminary data to suggest that the consumption of prebiotics can modulate immune parameters in GALT, secondary lymphoid tissues and peripheral circulation. Future protocols on the physiological impact of consuming prebiotics should be designed to include assessments of the gut microflora, gut physiology and the function and composition of the various regions of GALT.