We have reported that rebamipide, a gastroprotective drug, suppresses indomethacin-induced gastric mucosal injury in humans and rats. However, the mechanisms of the cytoprotective actions of rebamipide have not been fully addressed. In the present study, we determined mRNA expression profile of the gastric mucosa treated with indomethacin in rats, and investigated the cytoprotective effects of rebamipide against indomethacin-induced injury with a high-density oligonucleotide array (Rat Toxicology U34 GeneChip array). Gastric epithelial cells were obtained by laser-assisted microdissection. Data analysis was performed with a GeneChip Operating Software, GeneSpring software 7.0, and Ingenuity Pathway Analysis. Among 1,031 probes, the expression of 160 probes (15.5%) showed at least 2.0-fold up-regulation (158 probes) and down-regulation (2 probes) 2 h after indomethacin administration in comparison with the vehicle-treated rats. The pathway analysis of the up-regulated 123 probes identified the network with a highly significant score, which consisted of known clusters of cell death, cancer, and endocrine system disorders. We succeeded in listing 10 genes that were up-regulated by the treatment with indomethacin and that were down-regulated by rebamipide, including growth arrest and DNA damage-induced 45alpha. In conclusion, we demonstrated that cell death, especially apoptosis, pathway is involved in the pathogenesis of indomethacin-induced gastric mucosal injury, and that inhibition of apoptosis-related genes is possibly important for the cytoprotective effect of rebamipide against this injury.