Currently, the main difficulty in the accurate diagnosis of inflammatory bowel disease (IBD) is associated with the high prevalence of infectious, allergic and autoimmune diseases leading to intestinal lesions mimicking IBD. In geographical regions where there is endemicity for certain infections, in particular tuberculosis, timely verification of the diagnoses of ulcerative colitis (UC) and Crohn’s disease (CD) is a serious problem. Some infectious, allergic and autoimmune pathologies can not only imitate the clinical and endoscopic picture of IBD, but also complicate the course of an existing IBD, as a result of which there is resistance to the prescribed basic therapy in patients with UC and CD. Unfortunately, the complexity and limited possibilities of diagnostic methods can often be the reason for the belated establishment of an accurate diagnosis. Thus, in all these diseases, the main fecal markers for verifying the diagnosis of IBD, fecal calprotectin and lactoferrin, often have elevated values.