Probiotics are defined as live bacterial preparations with clinically documented health effects in humans. Probiotics have specific properties and targets in the human intestinal tract and intestinal microbiota. Each probiotic strain, independent of its genus and species is unique and, thus, the properties and the human health effects of each strain have to be assessed in a case-by-case manner. Understanding the mechanisms by which probiotics influence the normal intestinal microbiota and counteract aberrancies in microbiota would facilitate the use of probiotics for both dietary management and reduction in risk of specific diseases. Development of intestinal microbiota is an important factor affecting the health of the newborn. Recent studies suggest that specific bacterial components, especially the bifidobacteria, have a key impact on development of a healthy balanced infant microbiota. The composition of infant and child intestinal microbiota may become aberrant and thus influence the development of diarrheal, inflammatory, and allergic diseases. Based on this understanding, positive health effects of probiotics have been reported in the management of diarrheal, inflammatory, and allergic diseases in infants. Most recently, a reduction in risk of atopic diseases followed early administration of specific probiotics.