Because strategies to manipulate gut microbiota have been considered to prevent the development of allergic diseases, prebiotics such as indigestible oligosaccharides could be possible candidates for allergy prevention agents. However, clinical trials to test this idea, as well as mechanistic studies, are quite limited. We, therefore, have investigated the allergy preventing action of indigestible oligosaccharides in rodent models. Dietary fructo-oligosaccharide (FOS) reduced 2,4-dinitrofluorobenzene-induced contact hypersensitivity in mice, and the action was associated with the proliferation of bifidobacteria in the gut. In addition, maternal consumption of FOS altered the composition of gut microbiota in the neonates and reduced the severity of atopic dermatitis-like skin lesions in the offspring of NC/Nga mice. These results suggest that dietary FOS reduces the development of allergic diseases by modulating gut microbiota. In contrast, although dietary raffinose and α -linked galacto-oligosaccharide reduced the allergic airway inflammation in ovalbumin-primed Brown Norway rats, the mechanisms might be independent of gut microbiota. Dietary FOS eliminated Candida albicans colonization in the colon, which we previously suggested as a risk factor for food allergies. We propose that indigestible oligosaccharides are allergy preventing luminacoides and that these rodent models are useful for the mechanistic studies.