Model Context Protocol (MCP) Server for Fast Healthcare Interoperability Resources (FHIR) APIs

Table of Contents

• Model Context Protocol (MCP) Server for Fast Healthcare Interoperability Resources (FHIR) APIs
  • Table of Contents
  • Overview
  • Demo
    • Demo with HAPI FHIR server
    • Demo with EPIC Sandbox
  • Core Features
  • Prerequisites
  • Installation
    • Installing using PyPI Package
    • Installing from Source
    • Installing using Docker
      • Running the MCP Server with Docker
      • Using Docker Compose with HAPI FHIR Server
  • Integration with MCP Clients
    • VS Code
    • Claude Desktop
    • MCP Inspector
  • Configuration
    • CLI Options
    • Environment Variables
  • Tools
  • Development & Testing
    • Installing Development Dependencies
    • Running Tests

Overview

The FHIR MCP Server is a Model Context Protocol (MCP) server that provides seamless integration with FHIR APIs. Designed for developers, integrators, and healthcare innovators, this server acts as a bridge between modern AI/LLM tools and healthcare data, making it easy to search, retrieve, and analyze clinical information.

Demo

Demo with HAPI FHIR server

This video showcases the MCP server's functionality when connected to a public HAPI FHIR server. This example showcases direct interaction with an open FHIR server that does not require an authorization flow.

https://github.com/user-attachments/assets/cc6ac87e-8329-4da4-a090-2d76564a3abf

Demo with EPIC Sandbox

This video showcases the MCP server's capabilities within the Epic EHR ecosystem. It demonstrates the complete OAuth 2.0 Authorization Code Grant flow.

https://github.com/user-attachments/assets/96b433f1-3e53-4564-8466-65ab48d521de

Core Features

• MCP-compatible transport: Serves FHIR via stdio, SSE, or streamable HTTP

• SMART-on-FHIR based authentication support: Securely authenticate with FHIR servers and clients

• Response Filtering using FHIRPath: Filter resources and bundles returned by read and search operations using custom FHIRPath expressions to retrieve only the fields needed for the task, reducing payload sizes.

• Tool integration: Integratable with any MCP client such as VS Code, Claude Desktop, and MCP Inspector

Prerequisites

• Python 3.8+
• uv (for dependency management)
• An accessible FHIR API server.

Installation

You can use the FHIR MCP Server by installing our Python package, or by cloning this repository.

Installing using PyPI Package

1. Configure Environment Variables:

   To run the server, you must set FHIR_SERVER_BASE_URL.