In the present study, the phytoprotective effects of gypenosides from Gynostemma pentaphyllum throughout the gastrointestinal tract and kidney were examined in indomethacin-treated rats. Indomethacin induced gastric and intestinal damage as well as renal toxicity after a single toxicological dose (10 mg/kg) in rats. Acute oral administration of the gypenoside extract (200 mg/kg) significantly reduced gastric and intestinal toxicity induced by indomethacin as measured by ulceration, caecal haemoglobin and plasma haptoglobin. A significant decrease in small intestinal lactose fermenting enterobacteria was evident in animals treated with indomethacin and those pre-treated with G. pentaphyllum then indomethacin. In the renal system, kidney toxicity was evident after indomethacin and in animals pre-treated with indomethacin plus G. pentaphyllum with an increase in urinary N-acetyl-beta-glucosaminidase and a decrease in urinary sodium and chloride electrolyte output. However, a significant increase in urinary microprotein in indomethacin-treated animals was not present in indomethacin plus G. pentaphyllum-treated animals. These studies demonstrate the efficacy of Gynostemma pentaphyllum in lowering gastrointestinal damage induced by indomethacin. The results suggest further investigations of Gynostemma gypenosides are warranted to examine the mechanisms of this phytoprotective activity.