The invention relates to medicinal means on the basis of a peptide pharmaceutical composition for treatment of Helicobacter pylori-induced gastroduodenal diseases. The technical result of the invention consists in the peptide glutamyl-aspartyl-glycine with formula: H-Glu-Asp-Gly-OH revealing a specific activity manifested in an inhibiting effect on mitochondrial mechanisms of Helicobacter pylori-induced apoptosis in gastric epitheliocytes, which hinders the Helicobacter pylori influence on the cells and reduced apoptosis induction. Claimed is a pharmaceutical composition having a specific activity manifested in an inhibiting effect on mitochondrial mechanisms of Helicobacter pylori-induced apoptosis in gastric epitheliocytes, characterized in that it comprises an amount, effective on Helicobacter pylori, of the peptide with formula H-Glu-Asp-Gly-OH as the active substance, and a pharmaceutically acceptable carrier, as well as a use of the pharmaceutical composition for producing a means for treatment of Helicobacter pylori-induced gastroduodenal diseases, comprising an amount, effective on Helicobacter pylori, of the peptide with formula H-Glu-Asp-Gly-OH as the active substance, and a pharmaceutically acceptable carrier. According to the invention, the means comprised the active substance in the amount of 1 μg/kg to 10 μg/kg. According to the invention, the means exists in the form suitable for oral or parenteral administration. Claimed is a method for treatment of Helicobacter pylori-induced gastroduodenal diseases by inhibiting Helicobacter pylori-induced apoptosis in gastric epitheliocytes comprising administering to a subject in need thereof a means comprising an amount, effective on Helicobacter pylori, of the peptide with formula H-Glu-Asp- Gly-OH in the dose of 1 μg to 10 μg per 1 kg of body weight orally, daily, 3 times a day for 10-20 days, or parenterally, daily, once a day, for 10 days. According to the invention, the administration is performed orally or