Prebiotics have the potential to promote immediate and long-term effects on the health and well-being of infants. They have been added to infant formulas in Japan for 20 years and have only recently been used in Europe. The objective is to change the intestinal microflora in order to mimic the bacteriological effect and, thus, the functional effects of human milk. There is, however, a potential risk of long-term effects of the use of these infant formulas. The consequences of using prebiotics in infants, during the first months of life, on the composition and development of the intestinal microflora, and on the resulting bacterial–bacterial and bacterial–host interactions are not known. Attempts have been made to improve infant and follow-on formulas by prebiotic supplementation, but intervention studies are needed to evaluate their immediate and long-term beneficial effects and demonstrate the absence of harmful consequences from their use.