We compared the colonization of lactobacilli in the stomachs of mice fed nonpurified and purified diets and examined to determine whether the expression of Toll-like receptor 2, which is involved in the recognition of lactobacilli, is influenced by diet. Female BALB/c mice were fed a nonpurified or a purified diet for 2 weeks. Conventional cultivation and cultivation-independent molecular biological analysis based on the 16S rRNA gene sequence revealed that the number of lactobacilli associated with the gastric tissue was significantly higher in the mice fed the nonpurified diet than in those fed the purified diet. Sequencing analysis indicated that L. gasseri and L. johnsonii were predominant Lactobacillus species associated with the gastric tissue of the mice fed the nonpurified diet. The mRNA levels of Toll-like receptor 2, but not of 9, in the gastric tissue were significantly higher in the mice fed the purified diet than in those fed the nonpurified diet. We propose that nonpurified and purified diets have different impacts on gastric microbiota, which can in turn influence the expression of Toll-like receptor 2 in the stomach.