Momentum FHIR MCP Server

Open-source MCP server that connects Claude to any HL7 FHIR R4 server, adding document ingestion and semantic search on top of full FHIR CRUD.


Type	MCP server
Supplier	Momentum (open source)
Availability	GA
Pricing	Free / OSS (MIT). A Pinecone account is needed for the semantic-search / document tools
Capabilities	Read/Write — full FHIR R4 CRUD plus document ingestion and vector search
Verified	works · 2026-07-20
Security	caution · 2026-07-20 — provenance matches the-momentum/fhir-mcp-server, MIT, maintained, but write-capable over PHI and document/search tools ship clinical data to a third-party Pinecone account

How to install

Not published to PyPI — source install only. Clone, configure .env, and build with either Docker or uv:

git clone https://github.com/the-momentum/fhir-mcp-server
cd fhir-mcp-server
cp config/.env.example config/.env
make uv

(Edit config/.env to set your FHIR server base URL and, for the semantic-search tools, your Pinecone credentials.)

The server runs over stdio, so Claude launches the process itself — there is no long-lived service to keep running.

Claude Code — register the uv launch command (replace /path/to/fhir-mcp-server with the absolute path of your clone — e.g., $(pwd) if you’re still inside it from the clone step):
```
claude mcp add --transport stdio fhir-momentum -- uv run --frozen --directory /path/to/fhir-mcp-server start
```
Claude Desktop — add to claude_desktop_config.json (replace <your-project-path> with the absolute path of your clone, and <uv-bin-folder-path> with the directory containing the uv binary — find it with dirname $(which uv)):
```
{
  "mcpServers": {
    "fhir-momentum": {
      "command": "uv",
      "args": ["run", "--frozen", "--directory", "<your-project-path>", "start"],
      "env": { "PATH": "<uv-bin-folder-path>" }
    }
  }
}
```
A Docker launch is also documented upstream (make build, then a docker run … mcp-server:latest stdio entry) — see the README if you prefer containers. Restart Claude Desktop after editing the config.

What it does

Exposes FHIR resource handlers plus document and terminology tools:

FHIR resources — Patient, Observation, Condition, Medication, Immunization, Encounter, AllergyIntolerance, FamilyMemberHistory, and a generic resource handler, with full CRUD.
Document management — DocumentReference handling, AI-powered ingestion and chunking of multiple formats, and Pinecone-backed semantic search over ingested clinical documents.
Terminology — LOINC code retrieval.

Primary use cases: Natural-language search and retrieval over EHR/FHIR records, drafting and writing back FHIR resources, semantic search across clinical documents.

Notes

Distinct from the WSO2 FHIR MCP (a CRUD bridge to any FHIR server) and the Anthropic fhir-developer authoring plugin: Momentum adds document ingestion/chunking and Pinecone vector search, so it targets retrieval-augmented clinical workflows rather than bare resource CRUD. The semantic-search and document tools require Pinecone; the plain FHIR CRUD tools do not. stdio transport.

Sources

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