Abstract: Rare small intestinal diseases are characterized by a broad disease spectrum, non-specific clinical manifestations, and relatively limited diagnostic modalities, which significantly hinder early diagnosis and treatment. Meanwhile, the subspecialty development of rare digestive diseases lags behind, with insufficient physician awareness and a scarcity of experienced multidisciplinary collaborative teams, further exacerbating the difficulties in disease management. In recent years, advancements in gene testing technologies, along with continuous refinements in imaging and endoscopic techniques, have substantially improved the diagnostic and therapeutic landscape for rare small intestinal diseases. This article outlines the difficulties and challenges in diagnosing and treating these conditions, and reviews the evolving applications of common diagnostic and therapeutic approaches across various rare small intestinal diseases.