Chronic inflammatory bowel disease includes Crohn’s disease, ulcerative colitis, and unclassified colitis. In 20-25% of cases, the disease is diagnosed before the age of 18. Diagnostic criteria for diagnosing chronic diseases are usually defined, but none are exclusively specific. Because of that differential diagnosis includes a wide range of inflammatory diseases that can mimic Crohn's disease or ulcerative colitis. Diseases presented as IBD can be divided into monogenic, infectious or non-infectious diseases. Monogenic diseases arise as a result of a mutation in DNA that follows Mendel’s laws of inheritance. Today, about 163 gene loci are thought to be associated with chronic inflammatory bowel disease. Given the possible mechanisms of functioning, they can be divided into: epithelial barrier defects, neutropenia and defects in phagocytic bacterial killing, hyper- and autoimmune disorders, disorders affecting the selection and activation of T and B lymphocytes, disorders of immune dysregulation. Infectious diseases make up a large percentage of gastrointestinal diseases in children. Infections that present with symptoms similar to those of inflammatory bowel disease are intestinal tuberculosis, amoebiasis, lambliasis, infections caused by Clostridium difficile bacteria, Campylobacter, Salmonella, Yersinia as well as cytomegalovirus. It is important for us to discover the causes of these symptoms and signs because the treatment algorithms as well as the prognosis itself differ. The last group of diseases consists of non-infectious diseases. In early childhood, allergy to cow's milk is common, as well as intolerance to carbohydrate. Celiac disease is also possible. A detailed anamnesis and physical examination are important for a proper diagnosis. The findings were supplemented by laboratory, pathohistological and imaging tests and specific tests for diseases that we suspected.