The present study tested the persistence of orally administered bacteria in the gut of suckling mice. We used three bacterial strains: one strain of Lactobacillus johnsonii (designated strain Ms1) that was previously isolated from the mouse stomach, and two strains of L. plantarum, (strain No. 14 and JCM 1149T). We detected L. johnsonii Ms1, but neither strain of L. plantarum, in the gut 7 days after administration when the organisms were administered on days 0, 1, 3 or 7 of neonatal life. None of the strains was detected in the gut 7 days after the administration on days 14 or 28 of neonatal life. L. johnsonii Ms1 and L. plantarum JCM 1149T exhibited similar levels of in vitro association with gut tissues, with both strains showing association that was significantly higher than that of L. plantarum No. 14. In a separate experiment, the number of total bacteria and lactobacilli in the gut, as estimated by real-time quantitative PCR, was significantly higher in 14- and 21-day-old mice than in 0- and 7-day-old mice. In addition, the number of total bacteria was higher in 21-day-old mice than in 14-day-old mice, and the number of lactobacilli was higher in 7-day-old mice than in 0-day-old mice. These results suggest that gut persistence of administered bacteria in infant mice is species- or strain-specific and is affected by the development of indigenous microbiota. In addition, gut persistence of administered bacteria may not always depend on the tissue association capacity.