The dietary approach to reducing the risk of atopic diseases in infancy is evolving from passive allergen avoidance to active stimulation of the immature immune system, the aim of which is to support the establishment of tolerance. The intestinal mucosa and the mucosa-associated immune system are the primary loci of allergen contact and induction of immune responsiveness. In this review we discuss cross-talk between the intestinal microbiota and the host as it pertains to healthy immunologic maturation. Understanding these complex phenomena provides the rationale for the use of probiotics in reducing the risk and nutritional management of atopic disease.