In allergic enteropathy (gastrointestinal form of food allergy) in children, clinical symptoms can be often observed similar to the signs of celiac disease (persistent diarrhea and other dyspeptic symptoms, nutritive insufficiency), sensitization to gluten and a number of other food allergens, yet the prognosis for these diseases will be different. In order to specify the differential-diagnostic criteria of the latter, 38 children with allergic enteropathy and 72 patients with celiac disease were examined at various terms of their observance of gluten-free diets. The main differential-diagnostic criterion of allergic enteropathy as compared with celiac disease might be the absence of the dynamics of morphometric parameters of the mucous membrane of the small intestine and antibody titers to gluten depending on the presence or absence of gluten in the diet. Several months after administering a gluten-free diet a differential diagnosis of either allergic enteropathy or celiac disease will be difficult to make, in some cases, however, it is possible with the help of an analysis of morphometric indices of the mucous membrane considering the duration of dieting