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Establishing correct clinical thinking is the core and foundation of improving doctors' clinical ability as well as the key and difficult point of medical education. Different from common diseases, the clinical thinking of rare diseases has its unique characteristics. Taking dwarfism as an example, this paper summarizes the characteristics of diagnosis reasoning for rare diseases in the aspects of data collection, logical reasoning, evidence-based teaching, multiple disciplinary team, molecular biology research and artificial intelligence, which is conducive to improving the efficiency of physicians and providing experience for clinical thinking training of rare diseases.