A pharmaceutical compositions comprising saponin compounds selected from the group consisting of panaxytriol, panaxydol, panaxynol, ginsenoside Rc, Rb1, 20(S)-ginsenoside Rg3, 20(R)-ginsenoside Rg3, 20(S)-ginsenoside Rh2, 20(R)-ginsenoside Rh2, 20(R)-protopanaxadiol, 20(S)-protopanaxadiol, 20(S)-ginsenoside Rh1, 20(S)-protopanaxatriol and the mixture thereof, as an active ingredient in an amount effective to treat or prevent human or mammal gastro-intestinal diseases caused by abnormal proliferation of Helicobacter pylori, together with a pharmaceutically acceptable carrier.