AWS HealthLake MCP Server

Open-source MCP server that connects Claude to AWS HealthLake FHIR datastores for reading, searching, and (optionally) writing clinical resources, with automatic datastore discovery.

   
Type MCP server
Supplier AWS Labs
Availability GA — distributed on PyPI as awslabs.healthlake-mcp-server (Apache-2.0)
Pricing Free / OSS (Apache-2.0). Requires an AWS account; AWS HealthLake usage is billed by AWS, and FHIR data is HIPAA-eligible on AWS.
Capabilities Read/Write — full FHIR R4 CRUD, search, and bulk import/export; --readonly flag blocks all mutating operations
Verified works · 2026-07-20
Security cleared · 2026-07-20 — PyPI awslabs.healthlake-mcp-server 0.0.16 Apache-2.0, provenance matches AWS Labs, maintained, no OSV advisories; PHI/write-capable

How to install

  • Claude Code — direct stdio add via uvx (requires uv installed):

    claude mcp add --transport stdio healthlake --env AWS_REGION=us-east-1 --env AWS_PROFILE=your-profile-name -- uvx awslabs.healthlake-mcp-server@latest

    (replace your-profile-name with a configured AWS CLI profile, and us-east-1 with the region hosting your HealthLake datastore. Add --readonly after @latest — i.e. -- uvx awslabs.healthlake-mcp-server@latest --readonly — to disable writes.)

  • Claude Desktop — add to claude_desktop_config.json:

    {
  "mcpServers": {
    "healthlake": {
      "command": "uvx",
      "args": ["awslabs.healthlake-mcp-server@latest"],
      "env": {
        "AWS_REGION": "us-east-1",
        "AWS_PROFILE": "your-profile-name",
        "MCP_LOG_LEVEL": "INFO"
      }
    }
  }
}

    This is a stdio server — Claude Desktop/Code launches the uvx process itself, so there is no long-running service to keep open in a separate terminal. (To verify the server boots before wiring it up, run uvx awslabs.healthlake-mcp-server@latest once in a terminal and Ctrl-C after it initializes.)

  • Docker — pre-built image, credentials passed as environment variables:

    docker run -e AWS_ACCESS_KEY_ID=<key> -e AWS_SECRET_ACCESS_KEY=<secret> -e AWS_REGION=us-east-1 awslabs/healthlake-mcp-server

What it does

  • list_datastores, get_datastore_details — automatic discovery of available HealthLake datastores, exposed as MCP resources (no manual datastore-ID configuration).
  • read_fhir_resource, create_fhir_resource, update_fhir_resource, delete_fhir_resource — FHIR R4 CRUD by resource type and ID.
  • search_fhir_resources — advanced search: chained parameters, _include/_revinclude, modifiers, date/number prefixes, and pagination.
  • patient_everything — the FHIR $everything operation to pull a full patient record graph.
  • start_fhir_import_job, start_fhir_export_job, list_fhir_jobs — bulk import/export job management.

Primary use cases: EHR-backed cohort review, agentic clinical-data workflows over HealthLake, patient-record summarization, and bulk FHIR ETL orchestration.

Notes

Authentication uses AWS Signature V4 with standard credential resolution (IAM roles, AWS_PROFILE, or AWS_ACCESS_KEY_ID/AWS_SECRET_ACCESS_KEY env vars); the invoking principal needs HealthLake IAM permissions (healthlake:ListFHIRDatastores, healthlake:DescribeFHIRDatastore, and the FHIR resource actions). Use --readonly for production, audit, or compliance scenarios where writes must be blocked. AWS HealthLake is a HIPAA-eligible service, but a Claude configuration is only appropriate for PHI when covered under the applicable BAA and required settings — see Anthropic’s healthcare BAA guidance. Distinct from the vendor-agnostic FHIR MCP servers (WSO2, Momentum): this one is AWS HealthLake-specific and adds datastore discovery plus bulk import/export.

Sources

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