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These disorders are often rare and challenging to distinguish due to overlapping clinical, serological, endoscopic, and histopathological features. Through a systematic literature search using keywords such as small intestinal VA, malabsorption, and specific enteropathies, this review provides a comprehensive overview of diagnostic clues for VA and malabsorption. We systematically summarize the pathological characteristics of each condition to assist pathologists and clinicians in accurately identifying the underlying etiologies. Current studies still have many limitations and lack broader and deeper investigations into these diseases. 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