The article presents data referring difficulties in diagnosing Crohn’s disease. Literature data on prevalence, clinical manifestations, features of intestinal lesions, and extraintestinal manifestations of the disease are given. The common instrumental and morphological methods for Crohn’s disease diagnosis are discussed. We describe the medical history of a patient with Crohn’s disease manifested predominantly as a small intestine lesion. Subsequent thromboses of the portal, superior mesenteric and splenic veins, spleen, thromboembolism of the middle and small branches of the pulmonary arteries significantly complicated the path to a proper diagnosis.