The underlying denominators and treatment targets in atopic disease may be outlined as aberrant barrier functions of the skin epithelium and gut mucosa, and dysregulation of the immune response to ubiquitous environmental antigens. The route of sensitization varies with age, dietary antigens predominating in infancy. The immaturity of the immune system and the gastrointestinal barrier may explain the peak prevalence of food allergies at an early age. Dietary methods to control symptoms and reduce the risk of allergic disease have hitherto focused on elimination diets, alone or in combination with other environmental measures. The results have not been satisfactory regarding long-term prevention, primary or secondary. In view of the increasing burden of the abnormalities, new approaches are urgently needed for the management of allergic diseases and their prevention in at-risk infants. Novel methods here may include probiotics to counteract the immunological and gut mucosal barrier dysfunction associated with allergic disease, and thereby to strengthen endogenous defence mechanisms. Notwithstanding the demonstrations of important immunoregulatory potential of the well-balanced gut microbiota, the major objective health benefits of specific strains in allergic infants have only recently been clinically proven. Advances here have prompted enthusiasm in the scientific community and food industry and have fuelled research activities currently focusing firstly on identification of specific strains with anti-allergenic potential, and secondly on the question how food matrix and dietary content interact with the most efficacious probiotic strains.