BACKGROUND: Establishment of the gut microbiota at birth provides a substantial source of microbial stimuli for the maturation of the immune system. Deviations in this process precede the development of specific diseases providing the rationale for the use of probiotics to counteract them. OBJECTIVE: This study was designed to characterize both the mother-infant bifidobacteria transfer at birth and the development of bifidobacteria microbiota during the first weeks of life in infants whose mothers received Lactobacillus rhamnosus GG or placebo. METHODS: Species-specific PCR was used to assess the fecal bifidobacterial composition of mothers before and after delivery and in infants at 5 days and 3 weeks of age. RESULTS: Bifidobacterium longum was the species most commonly found in the mothers. Bifidobacterium catenulatum was the most prevalent group in infants at 5 days of age and B. longum the predominant species at 3 weeks. At 5 days of age, infants whose mothers received L. rhamnosus GG showed a significantly higher occurrence of B. breve and lower of B. adolescentis than those from the placebo group. In addition, L. rhamnosus GG consumption increased the bifidobacterial diversity in infants and reduced the Bifidobacterium microbiota similarity between mother and infant. CONCLUSIONS: These results indicate that specific changes in the transfer and initial establishment of bifidobacteria in neonates take place as consequence of the consumption of L. rhamnosus GG by the mothers.