A cohort of 197 infants was followed up prospectively for a single rotavirus (RV) season, 1983 to 1984, to examine the effect of long-term feeding method on RV infection. The feeding classification distinguished breast vs formula milk intake over the long term, for at least 18 weeks from birth (approximately four months). During the follow-up period, relative numbers of RV particles in feces were compared by electron microscopy, and positive specimens were confirmed by an enzyme-linked immunosorbent assay. There was no apparent difference in the infection rates of rotavirus enteritis in breast-fed (20%) as compared with bottle-fed (17%) infants. However, clinical manifestation of illness was milder in breast-fed infants. Among the breast-fed subjects, fecal flora identified by bacterial cultures, biochemical reaction, and gas-liquid chromatography revealed a significant growth of bifidobacteria lasting as long as the period of lactation. Colonization by this organism above the detection level of log 10(5)/mL was not observed in the feces of bottle-fed infants. These data suggest that alterations in enteric flora induced by breast-feeding may be correlates of intraluminal events, mediated by human milk, that modulate the clinical course of RV gastroenteritis.