The present study was conducted to evaluate the effects of early administration of Lactobacillus fermentum I5007 on intestinal development and microbial composition in the gastrointestinal tract using a neonatal piglet model. Full-term 4 day old piglets, fed with milk replacer, were divided into a control group (given placebo of 0.1% peptone water) and a L. fermentum I5007 group (dosed daily with 6 × 10(9) CFU/mL L. fermentum I5007). The experiment lasted 14 days. On day 14, a significant increase in the jejunum villous height (583 ± 33 vs 526 ± 18) and increases in the concentrations of butyrate (7.55 ± 0.55 vs 5.33 ± 0.39) and branched chain fatty acids in the colonic digesta were observed in piglets in the L. fermentum I5007 treatment (P < 0.05). mRNA expression of IL-1β (1.29 ± 0.29 vs. 0.62 ± 0.07) in the ileum were lower after 14 days of treatment with L. fermentum I5007. Denaturing gradient gel electrophoresis (DGGE) revealed that L. fermentum I5007 affected the colonic microbial communities on day 14 and, in particular, reduced numbers of Clostridium sp. L. fermentum I5007 play a positive role in gut development in neonatal piglets by modulating microbial composition, intestinal development, and immune status. L. fermentum I5007 may be useful as a probiotic for application in neonatal piglets.