Objective: To identify the features of chronic gastroduodenal pathology in children with atopic dermatitis (AD) complicated by secondary mycotic infection.Methods: The examination of mucous membrane micro-biocenosis of stomach and duodenum was performed in 64 children aged 3–16 years with diseases of gastrointestinal tract and AD complicated by fungal infection. 45 out of 64 patients, having been under medical supervision, had a combined damage of skin and gastrointestinal tract with Candida fungi. In-depth clinical and mycological study was performed represented by esophagogastroduodenoscopy with biopsy of intestine mucous membrane. The detection of circulating candida antigens in blood serum was conducted with method of amperometric enzyme biosensor. Helicobacter pylori were detected using urease test.Results: Children with AD combined with secondary mycotic infection had a damage of the upper parts of gastrointestinal tract and skin with Candida fungi in 70.3% of cases. Gastroduodenitis accounted for 66.7%; peptic ulcer disease was 33.3% in the structure of gastrodudenal pathology. Candida albicans fungi were plated in 80 % of cases; all children had a candida antigen in the blood serum.Conclusions: Children with AD, complicated by mycotic infection, and chronic gastrodudenal pathology should be examined for candidiasis of upper parts of gastrointestinal tract. If there is a candidiasis they should be prescribed with systemic antimycotics and dietary adjustment.