azure-fhir

This MCP server provides a bridge to Azure Health Data Services FHIR by exposing standard MCP interfaces to interact with Azure FHIR resources. It supports common FHIR operations via the MCP toolset, including resource discovery, search, and access to standard FHIR resources like Patient, Observation, Medication, and more through the MCP protocol. The server can operate using a client credentials flow (default) or an OAuth on-behalf-of flow when integrated with FastMCP and the Azure OAuth proxy. Tools available include search_fhir for dictionary-driven searches and get_user_info (OAuth only) to reveal information about the authenticated Azure user. You can navigate the FHIR resources using URIs such as fhir://Patient/ to access all patients or fhir://Observation/{id} for a specific observation, with the MCP server translating these requests to the Azure FHIR backend.

Prerequisites:

• Python 3.13+ installed
• uv (FastAPI/uvicorn runner for MCP)
• Git to clone the repository

Step-by-step installation:

1. Clone the repository

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

2. Create and activate a virtual environment Linux/macOS:

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

Windows:

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

3. Install dependencies (editable mode for development)

pip install -e ".[dev]"

4. Copy and configure environment variables

cp .env.example .env

Edit the .env file to include your Azure FHIR details, for example:

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

5. Run the MCP server (examples assume development setup)

uv run azure_fhir_mcp_server

6. If you plan to use Claude Desktop or other integrations, update the Claude configuration to point at your local MCP server as demonstrated in the repo’s Claude configuration guidance.

Notes and tips:

• The default authentication flow is client credentials; switch to OAuth On-Behalf-Of by enabling USE_FAST_MCP_OAUTH_PROXY=true and HTTP_TRANSPORT=true when using the FastMCP Azure OAuth proxy.
• Ensure fhirUrl, clientId, clientSecret, and tenantId are correctly set in your environment before starting.
• The mcp.json guidance in the README shows an example where the server is exposed via stdio (uvx) and can be executed from the MCP runtime with the azure-fhir-mcp-server entry point.
• Available tools include search_fhir for dictionary-based FHIR searches and get_user_info (OAuth only) for user metadata. Resource access is exposed through fhir:// URIs for standard FHIR resources.
• If you enable HTTP transport for OAuth, you may need to set FASTMCP_SERVER_AUTH_AZURE_BASE_URL and related redirect settings to match your deployment.