Inhibition of cyclooxygenase in the rat small intestine and gastric mucosa after subcutaneous administration of indomethacin has been investigated using prostacyclin (PGI2) production ex vivo as an index of prostaglandin biosynthesis. This has been compared with the formation of intestinal lesions and gastric erosions. Indomethacin caused marked inhibition of prostacyclin formation in the gastric mucosa, and this was accompanied by the development of gastric erosions, although after 48 h both inhibition of cyclooxygenase and gastric erosions were no longer apparent. There was no such temporal relationship between prostaglandin inhibition and the formation of lesions in the small intestine since the lesions became macroscopically apparent and developed at a time when cyclooxygenase inhibition was already declining. Aspirin caused a prolonged inhibition of small-intestinal cyclooxygenase activity, yet failed to cause intestinal damage. Thus, inhibition of prostaglandin synthesis alone may not be sufficient to initiate the processes which ultimately result in intestinal lesions. The prostaglandin-independent processes affected by indomethacin which lead to intestinal damage are as yet unknown.