The establishment of the faecal flora of 39 full-term infants fed exclusively on breast milk (n = 20) or with two different modern adapted cow's milk formulas (n = 19) was studied during the first 3 months of life. One formula investigated was based on 100% bovine casein as the protein source whereas the other formula contained bovine milk proteins with a whey/casein ratio of 60:40. A faecal flora rich in bifidobacteria was found in all study groups; the growth of putrefactive bacteria (especially Bacteroides spp.), however, was limited. In formula-fed infants, significantly higher bacterial counts of enterococci and clostridia were detected compared to breast milk-fed infants. Similarities and differences due to the feeding regimen were particularly reflected in the pattern of the anaerobic bacterial species. Bifidobacterium bifidum, B. infantis and B. breve constituted the majority of the bifidobacterial flora independent of the type of milk feeding. Other bifidobacterial species such as B. longum, B. adolescentis, B. parabifidum and B. pseudo-catenulatum were detected in high numbers and at low frequencies in breastfed infants. The latter three were observed in infants fed the whey/casein formula as well. It seems that infants fed a casein formula develop a faecal flora more like that of breastfed infants concerning Lactobacillus spp. (especially L. fermentum and L. brevis).