To investigate the effects of fermented formula (FF) with Bifidobacterium breve C50 and Streptococcus thermophilus 065 on thymus size and stool pH of healthy term infants, ultrasound examinations and evaluations of thymus sizes and thymus indices (TI) and measurements of stool pH were performed in the same 90 term neonates on the 3rd d of life and on the 1st, 2nd, 3rd, and 4th mo of life. Thirty newborns were exclusively breast-fed while the remaining 60 were randomly assigned to receive either a FF or a standard formula (SF). The fecal pH of the breast-fed group was lower than the SF group (p < 0.05), although it was similar to that of the FF group on the third postnatal day, persisting for the entire 4 mo of the study. The difference in TI was statistically significant over repeated measurements among the groups. The FF infants showed a TI similar to the breast-fed newborns. Probiotic fermentation products have effects comparable to those of the bacteria composing the intestinal microflora supporting the idea that intestinal bacterial balance plays an important role in improving host immune responses.