Azure AHDS FHIR MCP Server

An MCP server implementation for interacting with Azure Health Data Services FHIR.

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.

See the FastMCP guidance onmcp.jsonhere:https://gofastmcp.com/integrations/mcp-json-configuration

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

The OAuth on-behalf-of flow requires a confidential Azure AD application that represents the MCP server.
- In the Azure portal, go toMicrosoft Entra ID ➜ App registrations ➜ New registration. Give it a descriptive name such asFHIR-MCP-Server, setSupported account typestoSingle tenant, and leave the redirect URI unset for now.
- After the app is created, capture the generatedApplication (client) IDandDirectory (tenant) IDfor later use.
- UnderExpose an API, selectSetfor the Application ID URI and accept the suggested valueapi://{appId}. Add a scope nameduser_impersonationwith admin consent display/description also set touser_impersonation.
- UnderCertificates & secrets, create aNew client secret(for exampleFHIR-MCP-Secret-New). Copy the secret value immediately; it is required for the MCP serverclientSecretsetting.
- UnderAuthentication, add the following Web redirect URIs to support the FastMCP OAuth proxy:

- http://localhost:9002/auth/callbackEnsureDefault client typeremainsNoso the app stays confidential.

- SetUSE_FAST_MCP_OAUTH_PROXY=true
- RequiresHTTP_TRANSPORT=true

uv pip install -e . uv run --env-file .env azure-fhir-mcp-server

{ "mcpServers": { "fhir": { "type": "http", "url": "http://localhost:9002/mcp" } } }

The following is a table of available environment configuration variables:

- search_fhir- Search for FHIR resources based on a dictionary of search parameters
- get_user_info- (OAuth only) Returns information about the authenticated Azure user

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...

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

2 - Create and activate virtual environment:

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

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

4 - Copy and configure environment variables:

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

Openclaude_desktop_config.jsonand 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" } } } }

# Run all tests python -m pytest tests/ -v # Run with coverage pytest tests/ --cov=src/azure_fhir_mcp_server # Run specific test pytest tests/test_fastmcp_metadata.py::TestFastMCPMetadata::test_fastmcp_server_discovery -v # Run with detailed output pytest tests/test_fastmcp_metadata.py::TestFastMCPMetadata::test_output_detailed_metadata -v -s

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

Licensed under MIT - seeLICENSE.mdfile.

A healthcare MCP server for EMRs like Cerner and Epic, providing tools to interact with FHIR data and medical resources.