The purpose of this study was to evaluate the intensity of gastric inflammatory changes in atopic patients infected with H. pylori, and to find out whether a long-term exposure to a sensitizing allergen intensified the acuteness of inflammatory changes. The examinations were performed on patients with atopic diathesis who suffered from dyspepsia and gastralgia. The examined group included 72 women between 16 and 57 years of age (mean age: 36.5 years) and 38 men from 16 to 60 years of age (mean age: 34.4 years). The control group included 40 patients with no traits of atopy (13 men and 27 women between 18 and 56 years old, mean age: 34.8 years) with chronic gastritis confirmed by endoscopic and histopathological tests. All patients were subjected to endoscopy of the upper alimentary tract. Biopsy specimens were taken for histopathological analyses. They were stained with eosin and hematoxylin (the H&E method), and with a modified Giemsa method. The evaluation included the presence of chronic inflammation of gastric mucosa, its activity and intensity. The presence of H. pylori colonization was determined with the use of histopathological method of staining. Significant differences were found concerning inflammation intensity in atopic patients additionally infected with H. pylori, in comparison with the group of patients with food allergy without bacterial colonization. The differences were found during the evaluation of mucosa of both the prepyloric area and body of the stomach (p < 0.001). Moreover, statistically significant differences were found in the inflammation intensity between the examined group and the control group with no symptoms of allergy. In atopic patients infected with Helicobacter pylori, a long-term exposure to food allergens increases the intensity of gastric mucosa inflammation.