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The field of AI healthcare has undergone a significant transformation with the advent of large language models (LLMs), yet the challenges of interpretability within these models remain largely unaddressed. This study introduces **Chain-of-Diagnosis (CoD)** to enhance the interpretability of medical automatic diagnosis. CoD transforms the diagnostic process into a diagnostic chain that mirrors a physician’s thought process, providing a transparent reasoning pathway. Additionally, CoD outputs the disease confidence distribution to ensure transparency in decision-making. This interpretability makes model diagnostics controllable and aids in identifying critical symptoms for inquiry through the entropy reduction of confidences. With CoD, we developed **DiagnosisGPT**, capable of diagnosing 9,604 diseases for validating CoD. Experimental results demonstrate that DiagnosisGPT outperforms other LLMs on automatic diagnostic tasks across three real-world benchmarks. Moreover, DiagnosisGPT provides interpretability while ensuring controllability in diagnostic rigor.