Changes in the oral mucosa can appear in the course of inflammatory bowel disease in both children and adults. They often precede the appearance of gastrointestinal symptoms. The aim of the study was to determine the nature of changes in the oral cavity at the time of diagnosis of inflammatory bowel disease in children compared to children without systemic diseases. 49 children diagnosed with inflammatory bowel disease and 60 children without systemic diseases were examined. The prevalence of the aphthae stomatitis and angular cheilitis was 24.5% in the examined group and 10% in the control group (p = 0.0772). Changes in the oral mucosa occurred more frequently in children with Crohn's disease 35.3% than with ulcerative colitis 18.7%. In children with Crohn's disease, the most frequently observed lesion was aphthous stomatitis 23.5%, and in ulcerative colitis, angular cheilitis 12.5%. Changes in the oral mucosa are a therapeutic problem requiring in general diseases patients both local and systemic treatment and interdisciplinary cooperation between dentists, paediatricians and gastroenterologists. The finding of repeated changes in the oral mucosa during a dental examination should be the reason for referring the patient to a paediatrician for the foreclosure or make a diagnosis of inflammatory bowel diseases.