The overall purpose of this study was to examine the lactobacilli and bifidobacteria microbiota in the human ileum at a very early stage of life. Ileostomy effluents from two infants, taken at different time points, were plated on Lactobacillus selective agar and cys-MRS containing mupirocin to select for bifidobacteria. In one case, a stool sample following ileostomy reversal was subsequently analyzed microbiologically. Pulse-field gel electrophoresis and 16S rRNA sequencing was used to investigate the cultivable population of bifidobacteria and lactobacilli and denaturing gradient gel electrophoresis (DGGE) to examine the non-cultivable population. The probiotic strain, Lactobacillus paracasei NFBC 338, was recovered at both time points from one of the infants and dominated in the small intestine for a period of over 3 weeks. Moreover, the probiotic strain, B. animalis subsp. lactis Bb12, was obtained from the other infant. This study shows the presence of two known probiotic strains in the upper intestinal tract at an early stage of human life and thus provides some evidence for their ability to colonize the infant small intestine.