Weaning during infancy refers to the initiation of complementary food to breast milk. During weaning, there are significant changes on the gastrointestinal microbiota. Deleterious alterations of the gastrointestinal microbiota can result in pathological processes while measures that stimulate its development and stability, like the use of probiotics, are beneficial. The mechanisms by which probiotics achieve their effects have not been clearly established. Present work compares the microbial composition of feces from infants that were weaned to regular family food, formula with probiotics (B. Lactis BL y S. Thermophilus) or formula without probiotics. Accordingly, analysis of rDNA of microbial fecal samples by molecular techniques was used. Formula with or without probiotics was well tolerated and safe for all participating children. Probiotics present in formula were viable and susceptible to culture. There was not difference on physical growth or development among all participants. The microbiota of children supplemented with formula with- or without probiotics was different than that observed in children supplemented with regular food. It was not possible to determine enrichment of B. Lactis BL and S. Thermophilus in the feces of children that consumed the probiotics. Present work contributes to the understanding of probiotics effects in human health.