Abstract: There is a wide variety of rare intestinal diseases, presenting with various clinical manifestations. However, due to their low incidence rates, the diagnosis, drug development, and treatment of these diseases face greater challenges compared to common diseases. With the continuous deepening of clinical practice and the advancement of cutting-edge medical technologies, an increasing number of rare intestinal diseases can now be diagnosed and effectively treated. This article explores the classification and characteristics of rare intestinal diseases, the difficulties and countermeasures in clinical practice, as well as the challenges and opportunities in frontier research, aiming to provide references for gastroenterologists in the early identification, standardized diagnosis and treatment, and research directions of rare intestinal diseases.