Effects of indomethacin and cysteamine on the duodenal mucosa of rats were studied microscopically (using scanning electron microscopy) and also functionally. Indomethacin (5 mg/kg, s.c.) induced no microscopic damage to the duodenal epithelium for up to 6 hr after administration. Indomethacin had no effects on gastric H+ output and the amount of H+ in the duodenum, but did reduce the duodenal HCO3- secretion (both basal and 10 mM-HCl stimulated). PGE2 contents in the duodenal mucosa were markedly reduced by indomethacin for 6 hr. These results suggest that reductions of duodenal HCO3- secretion and endogenous prostaglandins per se do not impair the H+ disposal system of the duodenum and so do not damage the epithelial cells. In contrast, cysteamine (100 mg/kg, s.c.) produced microscopic damage to the duodenal epithelium as early as 2 hr later. Cysteamine significantly increased gastric H+ output and reduced duodenal HCO3- secretion, resulting in an increased amount of H+ in the duodenum 3 hr later. Cysteamine had no effect on PGE2 contents in the duodenum. The time lag between damage formation and functional changes suggests that the earliest damage caused by cysteamine occurs by mechanisms other than erosive action of H+ emptied by the stomach. The increased amount of H+ may contribute to an enhancement of the initial damage.