An MCP server that provides seamless integration with FHIR API, acting as a bridge between AI/LLM tools and medical data for searching, retrieving, and analyzing clinical information.

Installation

PyPI Package

uvx fhir-mcp-server

From Source

git clone <repository_url>
cd <repository_directory>
uv venv
source .venv/bin/activate
uv pip sync requirements.txt
uv run fhir-mcp-server

Docker

docker pull wso2/fhir-mcp-server:latest
docker run --env-file .env -p 8000:8000 fhir-mcp-server

Docker Compose

docker-compose up -d

Configuration

Claude Desktop - Streamable HTTP

{
    "mcpServers": {
        "fhir": {
            "command": "npx",
            "args": [
                "-y",
                "mcp-remote",
                "http://localhost:8000/mcp"
            ]
        }
    }
}

Claude Desktop - STDIO

{
    "mcpServers": {
        "fhir": {
            "command": "uv",
            "args": [
                "--directory",
                "/path/to/fhir-mcp-server",
                "run",
                "fhir-mcp-server",
                "--transport",
                "stdio"
            ],
            "env": {
                "FHIR_SERVER_ACCESS_TOKEN": "Your FHIR Access Token"
            }
        }
    }
}

VS Code - Streamable HTTP

"mcp": {
    "servers": {
        "fhir": {
            "type": "http",
            "url": "http://localhost:8000/mcp",
        }
    }
}

Available Tools

Tool	Description
`get_capabilities`	Retrieves metadata about a specific FHIR server

Features

MCP-compatible transport via stdio, SSE, or streamable HTTP
SMART-on-FHIR authentication support for secure connection to FHIR servers
Tool integration with VS Code, Claude Desktop, and MCP Inspector
OAuth 2.0 Authorization Code Grant flow support
Integration with Epic EHR ecosystem and HAPI FHIR servers

Environment Variables

Required

FHIR_SERVER_BASE_URL - Base URL of the FHIR server

Optional

FHIR_SERVER_CLIENT_ID - OAuth2 client ID used for authorizing MCP clients with the FHIR server
FHIR_SERVER_CLIENT_SECRET - Client secret corresponding to the FHIR client ID
FHIR_SERVER_SCOPES - Space-separated list of OAuth2 scopes to request authorization from the FHIR server
FHIR_SERVER_DISABLE_AUTHORIZATION - When set to True, disables authorization checks on the MCP server
FHIR_MCP_HOST - Hostname or IP address that the MCP server should bind to
FHIR_MCP_PORT - Port on which the MCP server will listen for incoming client requests
FHIR_SERVER_ACCESS_TOKEN - Access token for authenticating requests to the FHIR server

Notes

Supports Python 3.8+, requires uv for dependency management. When running locally via Docker, authorization should be disabled by setting FHIR_SERVER_DISABLE_AUTHORIZATION=True. Includes demo integrations with HAPI FHIR server and Epic Sandbox.

FHIR MCP Server

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