Introduction: Helicobacter pylori plays the main role in the development of chronic pathology of the gastroduodenal area. Helicobacter pylori infects 25% of the population in developed countries and up to 90% in developing countries. The most virulent are CagA positive (+) strains of Helicobacter pylori, which cause an intense cellular response, i.e. inflammation of the stomach mucous membrane, cell proliferation and cell death. Material and methods: We examined 75 children, aged 10 to 18 years, with chronic gastroduodenal pathology associated with Helicobacter pylori. A morphological and morphometric study of the stomach mucous membrane was performed depending on the presence of cytotoxic strains of Helicobacter pylori. Results: In children infected with CagA (+) strains of Helicobacter pylori, active and deep chronic gastritis and gastroduodenitis [21 (28.00%), 20 (26.67%), respectively] were more common than in children with CagA (−) strains [10 (13.33%), 13 (17.33%), respectively]. Discussion: Morphological studies provide an opportunity to determine quantitative and qualitative changes in the mucous membrane of the stomach in gastroduodenal pathology associated with Helicobacter infection. This increases the quality of diagnosis and predicts the course of the disease. Conclusion: A morphological study has shown that the presence of cytotoxic strains of Helicobacter pylori contributes to more significant changes in the gastric mucosa in children with chronic gastroduodenal pathology.