EHR-MCP: Real-world Evaluation of Clinical Information Retrieval by Large Language Models via Model Context Protocol

Kanato Masayoshi; Masahiro Hashimoto; Ryoichi Yokoyama; Naoki Toda; Yoshifumi Uwamino; Shogo Fukuda; Ho Namkoong; Masahiro Jinzaki

arXiv · 2509.15957

EHR-MCP: Real-world Evaluation of Clinical Information Retrieval by Large Language Models via Model Context Protocol

Kanato Masayoshi·Masahiro Hashimoto·Ryoichi Yokoyama·Naoki Toda·Yoshifumi Uwamino·Shogo Fukuda·Ho Namkoong·Masahiro Jinzaki

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Abstract

Background: Large language models (LLMs) show promise in medicine, but their deployment in hospitals is limited by restricted access to electronic health record (EHR) systems. The Model Context Protocol (MCP) enables integration between LLMs and external tools. Objective: To evaluate whether an LLM connected to an EHR database via MCP can autonomously retrieve clinically relevant information in a real hospital setting. Methods: We developed EHR-MCP, a framework of custom MCP tools integrated with the hospital EHR database, and used GPT-4.1 through a LangGraph ReAct agent to interact with it. Six tasks were tested, derived from use cases of the infection control team (ICT). Eight patients discussed at ICT conferences were retrospectively analyzed. Agreement with physician-generated gold standards was measured. Results: The LLM consistently selected and executed the correct MCP tools. Except for two tasks, all tasks achieved near-perfect accuracy. Performance was lower in the complex task requiring time-dependent calculations. Most errors arose from incorrect arguments or misinterpretation of tool results. Responses from EHR-MCP were reliable, though long and repetitive data risked exceeding the context window. Conclusions: LLMs can retrieve clinical data from an EHR via MCP tools in a real hospital setting, achieving near-perfect performance in simple tasks while highlighting challenges in complex ones. EHR-MCP provides an infrastructure for secure, consistent data access and may serve as a foundation for hospital AI agents. Future work should extend beyond retrieval to reasoning, generation, and clinical impact assessment, paving the way for effective integration of generative AI into clinical practice.

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Kanato Masayoshi, Masahiro Hashimoto, Ryoichi Yokoyama, Naoki Toda, Yoshifumi Uwamino, Shogo Fukuda, Ho Namkoong, Masahiro Jinzaki. 2025-09-19. EHR-MCP: Real-world Evaluation of Clinical Information Retrieval by Large Language Models via Model Context Protocol. https://arxiv.org/abs/2509.15957

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