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Background: Existence of clinical and pathophysiological relationship between gastrointestinal disorders and components of the metabolic  syndrome  in adults has been  proved. Aim: To study morphological  and functional status of upper gastrointestinal tract  and  the  degree  of its contamination with Helicobacter pylori in children with metabolic   syndrome.  Materials  and  methods: We examined 274 children aged from 9 to 16 years. Group 1 included 144 children with metabolic syndrome, group 2, 80 patients  with obesity without metabolic  syndrome,  group  3, 50 normal weight children  with  various  gastrointestinal disorders. The assessments included esophagogastroduodenoscopy  with biopsy for morphological  and bacteriological  investigations. Results: The children from the groups 1 and 2 had significantly less complaints of pain in epigastric and pyloro-duodenal area than  those  from the group  3 (15.2, 26.8 and54% of patients, respectively; р for comparison  of group  1 vs group  3 and group  2 vs group  3 were all < 0.05). Functional and structural abnormalities of upper gastrointestinal tract were found in 90.3,86.3 and 96% of children, esophagitis, in 19.4, 17.5 and  12%, respectively. Gastritis was significantly more frequent  in groups  1 and 2 than in group  3 (31.9, 37.5 and 14%, respectively, р for comparison of group 1 vs group 3 and group 2 vs group 3 were all < 0.05), whereas  in group  3 there  were  more cases of gastroduodenitis (37.5, 42.5 and 78%) and duodenal ulcers  (1.4, 2.5  and  8%,  respectively). Antral gastritis was diagnosed in 55.5, 45 and 40% of patients, stomach  erosions, in 5.6, 7.5 and 4%, duodenitis, in 44.4, 50 and 86%, bulbar erosions, in 2.8, 1.3 and 2%, active ulcers, in 1.4, 2.5 and 8%, cardia insufficiency in 33.3, 22.5 and 28%, duodeno-gastric  reflux, in 27.8, 26.3 and  24% patients from the  groups  1, 2 and  3, respectively. Gastric mucosal biopsies of most patients, irrespective of the groups (83.3, 87.5 and 77.3%), showed signs of active  chronic  gastritis. Various degrees  of contamination  with Н. pylori was found  in 61.5, 58.3 and 46.2% of children from the groups 1, 2 and  3, respectively. Conclusion: The rates of inflammatory abnormalities  in upper  gastrointestinal tract in all patient groups are similar (93–95%) and does not  depend on  bodyweight. Motor  and  evacuation  abnormalities  are  more  frequent  in obese children  than  in those  with normal  bodyweight, and do not depend on the  metabolic  syndrome. Children with metabolic  syndrome  are characterized by moderate degree  active chronic gastritis associated   with  Н. pylori,  with  minimal  clinical signs and  symptoms  and  predominance of focal rather than wide-spread inflammation.