Introduction: Breast-fed infants are generally found to have a typical intestinal flora with different bifidobacteria as the predominant species, which is considered to be important for the health of the infants. Recently, it has been described that allergic infants have a different flora compared to healthy infants. The levels of certain bifidobacteria species seem to be different and the levels of for example Bifidobacterium adolescentis are higher in allergic infants (1). Until now, the accurate determination of Bifidobacterium species in feces was impossible, but new molecular methods are now available, allowing the quantification of these species. Methods: For the accurate quantification of Bifidobacterium species in complex ecosystems, like the human gut, duplex 5′ nuclease assays (QRT-PCR) were developed for B. adolescentis, Bifidobacterium angulatum, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium catenulatum, Bifidobacterium dentium, Bifidobacterium infantis and Bifidobacterium longum. The assays, targeted on rRNA intergenic spacer regions, were tested on specificity, sensitivity, reproducibility and compared to conventional PCR methods described earlier. The validated QRT-PCR assays were subsequently used for determination of the relative amounts of different Bifidobacterium species in fecal samples of infants receiving a standard formula (SF) or a standard formula supplemented with galacto- and fructooligosaccharides (OSF). A breast-fed group was studied in parallel as a reference. Results: The results showed a significant increase in the total amount of fecal bifidobacteria in infants receiving the prebiotic formula (OSF). The bifidobacterial flora of these infants showed a large diversity of Bifidobacterium species similar to breast-fed infants, containing for example high numbers of B. infantis and B. longum. The intestinal flora of infants receiving a standard formula seems to resemble a more adult-like flora and contains relatively more B. catenulatum and B. adolescentis. Furthermore, the prevalence of B. adolescentis decreased significantly during the 6 weeks study period in the breast-fed group as well as in the group of infants receiving the prebiotic formula (OSF). Conclusion: With the use of newly developed QRT-PCR assays, the levels of bifidobacteria species in fecal samples can be determined accurately. From the current study it can be concluded that the prebiotic infant formula tested, stimulates different Bifidobacterium species in the infants’ colon, giving a distribution of the species that is comparable to the distribution in breast-fed infants.