Supplementation of formulas with prebiotics enhances the growth of lactate producing bacteria, and fecal lactate, and acetate levels in infants. High concentrations of organic acids in intestinal lumen have, however, been shown to impair the intestinal barrier function. To determine whether stimulating the colonic microbiotal metabolism with prebiotics would impair the neonatal intestinal barrier function, artificially reared rats were fed milk formula with or without a mixture of galactooligosaccharides/inulin (GOS/Inulin, 88/12; 5.6 g/L) from the 7th d of life (d7) until weaning (d20). At d18, GOS/inulin supplementation had increased the concentrations of acetate and lactate in colonic lumen. Although neither ileum-associated microbiota nor colonic permeability (assessed in Ussing chambers), nor the expression of tight junction claudin-2 and claudin-3 mRNA were altered, GOS/inulin supplementation was associated with increased bacterial translocation (BT) toward spleen. None of these effects persisted at d40. We conclude that GOS/inulin supplementation may increase BT in an immature gut. The balance between the potential infectious risk of BT vs. its putative beneficial effect on the maturation of neonatal immune system clearly warrants further study.