Azure AHDS FHIR MCP Server

Azure AHDS FHIR MCP Server 🚀

A Model Context Protocol (MCP) server implementation for Azure Health Data Services FHIR (Fast Healthcare Interoperability Resources). This service provides a standardized interface for interacting with Azure FHIR servers, enabling healthcare data operations through MCP tools.

Setup 🛠️

Installation 📦

Requires Python 3.13 or higher and uv.

Install uv first.

MCP Configuration ⚙️

Claude Desktop Configuration

1 - Edit Claude Desktop Configuration:

Open claude_desktop_config.json and add the following configuration.

On MacOs, the file is located here: ~/Library/Application Support/Claude Desktop/claude_desktop_config.json.

On Windows, the file is located here: %APPDATA%\Claude Desktop\claude_desktop_config.json.

{
    "mcpServers": {
        "fhir": {
            "command": "uvx",
            "args": [
                "azure-fhir-mcp-server"
            ],
            "env": {
                "LOG_LEVEL": "INFO",
                "fhirUrl": "https://your-fhir-server.azurehealthcareapis.com/fhir",
                "clientId": "your-client-id",
                "clientSecret": "your-client-secret",
                "tenantId": "your-tenant-id"
            }
        }
    }
}

The following is a table of available environment configuration variables:

Variable	Description	Default
`LOG_LEVEL`	Logging level	`INFO`
`fhirUrl`	Azure FHIR server URL	Required
`clientId`	OAuth2 client ID	Required
`clientSecret`	OAuth2 client secret	Required
`tenantId`	Azure AD tenant ID	Required

2 - Restart Claude Desktop.

Available Tools 🔧

FHIR Resource Operations

search_fhir - Search for FHIR resources based on a dictionary of search parameters

Resource Access

The server provides access to all standard FHIR resources through the MCP resource protocol:

fhir://Patient/ - Access all Patient resources
fhir://Patient/{id} - Access a specific Patient resource
fhir://Observation/ - Access all Observation resources
fhir://Observation/{id} - Access a specific Observation resource
fhir://Medication/ - Access all Medication resources
fhir://Medication/{id} - Access a specific Medication resource
And many more...

Development 💻

Local Development Setup

1 - Clone the repository:

git clone https://github.com/erikhoward/azure-fhir-mcp-server.git
cd azure-fhir-mcp-server

2 - Create and activate virtual environment:

Linux/macOS:

python -m venv .venv
source .venv/bin/activate

Windows:

python -m venv .venv
.venv\Scripts\activate

3 - Install dependencies:

pip install -e ".[dev]"

4 - Copy and configure environment variables:

cp .env.example .env

Edit .env with your settings:

fhirUrl=https://your-fhir-server.azurehealthcareapis.com/fhir
clientId=your-client-id
clientSecret=your-client-secret
tenantId=your-tenant-id

5 - Claude Desktop Configuration

Open claude_desktop_config.json and add the following configuration.

On MacOs, the file is located here: ~/Library/Application Support/Claude Desktop/claude_desktop_config.json.

On Windows, the file is located here: %APPDATA%\Claude Desktop\claude_desktop_config.json.

{
    "mcpServers": {
        "fhir": {
            "command": "uv",
            "args": [
                "--directory",
                "/path/to/azure-fhir-mcp-server/repo",
                "run",
                "azure_fhir_mcp_server"
            ],
            "env": {
                "LOG_LEVEL": "DEBUG",
                "fhirUrl": "https://your-fhir-server.azurehealthcareapis.com/fhir",
                "clientId": "your-client-id",
                "clientSecret": "your-client-secret",
                "tenantId": "your-tenant-id"
            }
        }
    }
}

6 - Restart Claude Desktop.

Contributions 🤝

Contributions are welcome! Please feel free to submit a Pull Request.

Fork the repository
Create your feature branch (git checkout -b feature/AmazingFeature)
Commit your changes (git commit -m '✨ Add some AmazingFeature')
Push to the branch (git push origin feature/AmazingFeature)
Open a Pull Request

License ⚖️

Licensed under MIT - see LICENSE.md file.

This is not an official Microsoft or Azure product.

You must be authenticated.

security – no known vulnerabilities

license - permissive license

quality - confirmed to work

remote-capable server

The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.

Tools

search_fhir

A Model Context Protocol server that enables standardized interaction with Azure Health Data Services FHIR servers, allowing healthcare data operations through MCP tools.

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