Development of the child's immune system tends to be directed toward a T-helper 2 (Th2) phenotype in infants. To prevent development of childhood allergic/atopic diseases, immature Th2-dominant neonatal responses must undergo environment-driven maturation via microbial contact in the early postnatal period. Lactic acid bacteria and bifidobacteria are found more commonly in the composition of the intestinal flora of nonallergic children. Epidemiological data also showed that atopic children have a different intestinal flora from healthy children. Probiotics are ingested live health-promoting microbes that can modify intestinal microbial populations in a way that benefits the host; and enhanced presence of probiotic bacteria in the intestinal microbiota is found to correlate with protection against atopy. There is insufficient but very promising evidence to recommend the addition of probiotics to foods for prevention and treatment of allergic diseases, especially atopic dermatitis. Clinical improvement especially in allergic rhinitis and IgE-sensitized (atopic) eczema has been reported too. Literature data for food allergy/hypersensitivity and asthma are not adequate for this guaranteed conclusion; however, clinical benefit of probiotic therapy depends on numerous factors, such as type of bacterium, dosing regimen, delivery method, and other underlying host factors, e.g., the age and diet of the host. The selection of the most beneficial probiotic strain, the dose, and the timing of supplementation still need to be determined. Accordingly, probiotics can not be recommended generally for primary prevention of atopic disease; and if probiotics are used in atopic infants/children for any reason, such as therapy or prevention, cautionary approach ought to be taken.