Jejunal Peyer's patches contain specialized epithelial M cells that take up ingested microorganisms from the lumen of the gut by transcytosis. Using DNA-micro array, we analyzed the gene expression patterns of jejunal Peyer's patches in order to gain insight into the molecular mechanism by which Lp6 interacted with the host organism in a gnotobiotic environment v. in the gut normal microflora. The micro array data revealed that, among approximately 14,000 genes, 420 were expressed in Lp6 administration group at twofold or higher levels compared to the control group. These included genes involved in immune response, and cell differentiation, cell-cell signaling, cell adhesion, signal transcription, and transduction. Real-time PCR confirmed the reliability of the analysis. These data indicated that administration of Lactobacillus Lp6 was associated with a complex genetic response in the jejunal Peyer's patches.