The aim of this study was to examine the influence of maternal intestinal and vaginal bifidobacteria on the establishment of bifidobacteria colonizing the gut in infants. Fecal samples from 110 healthy pregnant mothers within 1 mo before delivery and their babies at 1 mo of age and 100 vaginal swabs from the mother within 7 d before delivery were collected at a maternity hospital in Fukuoka city, Japan. The fecal and vaginal samples were assayed by PCR to detect Bifidobacterium species and by real-time PCR assays to estimate the bifidobacterial number. The detection of Bifidobacterium breve in the mothers' feces was significantly associated with increases in both the bifidobacterial counts and number of Bifidobacterium species in the babies' feces. In addition, a cesarean section was significantly associated with both a decrease in the counts and diversity of bifidobacteria in the babies' feces. The number of Bifidobacterium species detected in the vaginal swabs of mothers were not associated with either the bifidobacterial counts or the diversity of bifidobacteria in the babies' feces. The most important determinants of intestinal bifidobacteria in infants were the colonization of B. breve in the mothers' gut and vaginal delivery.