For infants, the introduction of food other than breast milk is a high risk period due to diarrheal diseases, and may be corroborated with a shift in the faecal microbiota. This longitudinal study was the first undertaken to understand the effect of the supplementation on the infant's faecal microbiota and particularly the bifidobacteria. Eleven infants were enrolled. Their faecal microbiota were analysed using temporal temperature gradient gel electrophoresis (TTGE) with bacterial and bifidobacterial primers. In parallel, bifidobacterial counts were followed using competitive PCR. Three periods were distinguished: exclusive breastfeeding (Bf period), weaning (i.e. formula-milk addition, W period) and postweaning (i.e. breastfeeding cessation, Pw period). The bifidobacterial counts were not modified, reaching 10.5 (Log10 cells g−1 wet weight). In the TTGE profiles, the main identified bands corresponded to Escherichia coli, Ruminococcus sp. and Bifidobacterium sp., more precisely Bifidobacterium longum, Bifidobacterium infantis and Bifidobacterium breve. For both TTGE profiles, the analysis of the distance suggested a maturation of the faecal microbiota but no correlation could be established with the diet. Despite a high interindividual variability, composition of the faecal microbiota appeared more homogenous after weaning and this point may be correlated with the cessation of breastfeeding.