Morphological and histopathological changes in the mucosa of the stomach, duodenum and small and large intestine have been evaluated in 83 children aged between 12 months and 15 years with diagnosed food allergy. The examined patients were analysed depending on clinical symptoms. Among 23 children aged 7-15 years, in whose clinical picture abdomen pains dominated, endoscopic examination of upper part of alimentary tract was performed. In 22 children (66.6%) macroscopic changes in stomach mucosa were observed. Histopathological examination of excisions from optically changed places showed variations in 13 children (39.3%). In 43 children aged 12 months--8 years with dominating symptoms of protracted diarrhoea and/or body mass deficiency, biopsy of small intestine mucosa was examined. In 13 children (30.2%) subtotal villus atrophy was observed, in 14 children (32.5%)--partial and in 16 children (37.3%) no small intestine mucosa atrophy was noticed. In all patients lymphocytic infiltrations occurred in small intestine mucosa lamina propria. Large intestine inflammation was observed in food allergy process in 7 children. In the cases of food allergy in children the inflammation changes in mucosa can be seen in all of its sections. Over 2/3 of examined children with food allergy showed inflammation and inflammation-atrophical changes in alimentary tract mucosa.