In the last decade, scientific studies in the field of children's gastroenterology performed in Lithuania explored different problems: pathology of Helicobacter pylori infection and food allergy. Our studies revealed that children with atopic dermatitis had gastrointestinal complaints (abdominal pain, diarrhea, distension and unstable stool, which appeared with the exacerbation of skin rash) more often as compared to nonallergic children of the control group. Abdominal pain in children with atopic dermatitis with local rash was more frequent and lasted longer than in control group children, whereas children with extended rash had stools more frequently. Gastrointestinal disorders in children with atopic dermatitis statistically significantly did not depend on the extent of skin rash and severity of atopic dermatitis. In our scientific research on the importance of H. pylori infection on children's gastrointestinal system, children with chronic dyspepsia were examined. Endoscopy, rapid urease test, biopsies from antrum and corpus of stomach and their histological examination as well as serologic tests were done. According to the results obtained, we recommend to examine children with chronic dyspepsia in a complex way: not only endoscopic examination, but H. pylori diagnostic tests should be performed as well. Serologic test is not suitable for screening H. pylori infection in children. Considering this, we recommend to use no fewer than two different methods to diagnose this infection. The highest frequency of H. pylori infection was found in children with duodenal ulcer; histological changes in their gastric pylorus and corpus mucosa were greatest. More than half of children with nonulcer dyspepsia were infected with H. pylori. After eradication of H. pylori infection, the prevalence of dyspepsia in children with duodenal ulcer decreased.