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It was examined 40 patients with atopic dermatitis in various stages of the clinical course of dermatosis. It has revealed typical endoscopic changes of the gastrointestinal tract in patients with atopic dermatitis in quiescent and acute stages. It has studied the cellular composition of infiltrates and histomorphology of mucous coat of stomach and distal part of sigmoid colon. It has found the generic dysbiotic malfunctions of intestinal microflora in different periods of the clinical course of dermatosis. It is suggested an assumption about the relations between morphological changes of mucous coat of stomach and distal part of sigmoid colon in patients with atopic dermatitis with symtomatic dysbiotic disorders of the intestine and the severity of skin lesions in atopic dermatitis.