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Today, in order to provide high-quality medical services and to extend resources and reduce costs, many large hospitals have adopted clinical guidelines as a structured way to manage medical activities. However, customization of clinical guidelines in order to treat a large number of patients is a major challenge. In this paper, we present a physician order category-based clinical guideline comparison system. The system uses a preprocessor software to convert the clinical guidelines from a Microsoft Word document into XML format, and it can also compare clinical guidelines over the conceptual view such as the physician order category. The system has already been used to compare the HCC surgical clinical guidelines of Taiwan and Mongolia-resulting in some differences being found, for which possible causes were discussed. Therefore, it can be seen that our research provides a practical and convenient way in which to compare clinical guidelines based on physician order category-thereby saving time and enabling physicians to quickly resolve discrepancies and make necessary adjustments to clinical guidelines.