Awareness of the key role of the intestinal microflora in the generation of the immunophysiological regulation and in the defence against pathogenic agents has attracted our interest in ways of manipulating the microbiota to improve health. Dietary modulation of the intestinal microflora is today one of the main topics of interest in the nutritional sciences. Performing this modulation in the neonatal or early infancy period, when immunological programming takes place, is a relatively new concept. Fructo-oligosaccharides (FOS) and galacto-oligosaccharides (GOS) are prebiotics whose bifidogenic activity has been proven in adults. However, only recently have they been combined in infant formulas to reproduce the prebiotic effect of human milk oligosaccharides. In two consecutive trials, it has been demonstrated that supplementation of infant formulas with a mixture of GOS and FOS modified the fecal flora of term and preterm infants, stimulating the growth of Bifidobacteria. In the trial with term infants, the bifidogenic effect of the prebiotic mixture was dose dependent and there was also a significant increase in the number of Lactobacilli in the supplemented group. These findings offer a promising horizon for the early prevention of allergy and infections in infants.