Probiotic bacteria are known for their beneficial effects on the intestinal immune function of the host animal. However, their effects on mucosal barrier function in chicks are not completely understood. The aim of this study was to determine the effects of the probiotic bacterium, Lactobacillus reuteri (LR), on the gastrointestinal mucosal barrier function of broiler chicks. One day-old male broiler chicks were orally injected water (300 μL) with or without 1× 10 8 cfu of LR (5 mg FINELACT, Asahi Calpis Wellness Co. Ltd.) every morning for 7 days (day 0 to 6). The crop, duodenum, ileum, and cecum were collected on day 7 and were used for histological analysis and RNA extraction. Then, the thickness of the mucosal structures and the number of goblet cells in the digestive tract were assessed using histological analysis. The expression of Mucin 2, factors related to the formation of tight junctions (Claudin1, 5, and 16, ZO2, and JAM2), cytokines (IL-6, CXCLi2, and IL-10), and avian β-defensin 10 (AvBDs) (AvBD2, 10, and 12) in the crop, duodenum, ileum, and cecum were analyzed using real-time polymerase chain reaction (PCR). Results showed that oral administration of LR increased ileal villus height and crypt depth, decreased Claudin16 level in the crop and increased JAM2 level in the crop and ileum, and decreased the expression of AvBD10 in the ileum and cecum and that of AvBD12 in the crop. It did not affect goblet cell number and Mucin 2 expression. These results suggested that LR used in this study may enhance mucosal barrier function by regulating tight junctions in the upper gastrointestinal tract.