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How to Connect FHIR R4 to Microsoft Copilot — via MCP

Any HL7 FHIR R4 server: search and read Patients, Observations, Conditions, Encounters, MedicationRequests, DiagnosticReports and any other resource type, plus the server's own capability statement. Bearer-token auth.

HCBy HelpCode teamUpdated 5 min read Open-source on GitHub
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FHIR R4

FHIR R4

Any HL7 FHIR R4 server: search and read Patients, Observations, Conditions, Encounters, MedicationRequests, DiagnosticReports and any other resource type, plus the server's own capability statement. Bearer-token auth.

tools

11

Region

INTL

Category

Healthcare

Authentication

Bearer Token

Required env vars

FHIR_BASE_URLFHIR_ACCESS_TOKEN
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    Open source · AGPL-3.0
  • Works with ChatGPT, Claude, Gemini
    Any MCP-compatible client

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Summary

Any HL7 FHIR R4 server: search and read Patients, Observations, Conditions, Encounters, MedicationRequests, DiagnosticReports and any other resource type, plus the server's own capability statement. Bearer-token auth.

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Example prompts for FHIR R4

Click any prompt to copy it. Paste into Claude, ChatGPT, Cursor, Gemini, Copilot or OpenClaw to run it against this connector.

FHIR R4 · live via MCP
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Claude is AI and can make mistakes. Please double-check responses.

💡 No install? Use cloud.anythingmcp.com directly. Sign in, click Connectors → FHIR R4, paste your credentials, mint an MCP API key — done. No Docker, no git clone, no local server.

FHIR R4 + Microsoft Copilot

Any HL7 FHIR R4 server: search and read Patients, Observations, Conditions, Encounters, MedicationRequests, DiagnosticReports and any other resource type, plus the server's own capability statement. Bearer-token auth.

Prerequisites

See the full setup instructions baked into the connector (visible in the in-app store when you select the connector). The required environment variables for this connector are:

FHIR_BASE_URL, FHIR_ACCESS_TOKEN

Step 1 — Get credentials

This is a generic FHIR R4 client, not a vendor connector. Point it at any R4 server — a hospital's HAPI instance, a national test server, a vendor's sandbox — and it speaks the standard.

  1. Set FHIR_BASE_URL to the server's base, the URL that answers /metadata. No trailing slash.
  2. Set FHIR_ACCESS_TOKEN to a bearer token. Most real deployments use SMART on FHIR, whose authorisation flow issues short-lived tokens; obtain one and paste it here, or use a long-lived service token if the server offers one. A server that needs no auth still needs a placeholder here — put anything.

…(continued in the in-app connector instructions)

Step 2 — Install the adapter

curl -fsSL https://raw.githubusercontent.com/HelpCode-ai/anythingmcp/main/docker-compose.quickstart.yml -o docker-compose.yml
printf 'JWT_SECRET=%s\nENCRYPTION_KEY=%s\n' "$(openssl rand -hex 32)" "$(openssl rand -hex 32)" > .env
docker compose up -d

Step 3 — Add the connector in Microsoft Copilot

Your server URL: in AnythingMCP, open MCP Servers → the server this connector is on, and copy its URL (https://cloud.anythingmcp.com/mcp/…). Use it wherever this guide shows YOUR_SERVER_ID.

Microsoft Copilot uses MCP servers through agents built in Copilot Studio: you add AnythingMCP to an agent as a tool, then publish the agent to Microsoft 365 Copilot and Teams. Copilot Studio connects from Microsoft's cloud over Streamable HTTP, which AnythingMCP supports.

  1. In Copilot Studio, open your agent (or create one), go to Tools and choose Add a tool → New tool → Model Context Protocol.
  2. Enter a Server name (for example AnythingMCP), a Server description that says what the connector does, and the Server URL https://cloud.anythingmcp.com/mcp/YOUR_SERVER_ID. Copilot Studio uses the description to decide when to call the server.
  3. Under authentication, choose API key, set Type to Header and the header name to X-API-Key, then select Create.
  4. In Add tool, choose Create a new connection, paste an MCP API key from AnythingMCP (MCP Servers → your server → API keys) and select Add to agent.
  5. Try it in the agent's Test pane: ask for something that needs the FHIR R4 tools.
  6. Select Publish, then Channels → Microsoft 365 and Microsoft Teams, keep Make agent available in Microsoft Copilot selected and choose Add channel. See agent in Teams installs it for you; in Microsoft 365 Copilot, type @ and pick the agent.

Prefer per-user sign-in? Choose OAuth 2.0 → Dynamic discovery instead of an API key: each user then signs in to AnythingMCP the first time the agent calls it.

Self-hosting? Use your instance's public HTTPS address instead of https://cloud.anythingmcp.com. Copilot Studio connects from Microsoft's cloud, so localhost does not work.

Available tools

ToolWhat it does
fhir_get_capability_statementRead the server's CapabilityStatement: which resource types it holds, which interactions and search parameters each supports, and its FHIR v
fhir_searchSearch any resource type with FHIR's standard parameters
fhir_read_resourceRead one resource instance by type and id, returning the full resource rather than a Bundle entry
fhir_search_patientsSearch Patients by name, identifier, birth date or family name
fhir_get_patient_observationsRead the Observations recorded for one patient — vital signs, laboratory results, measurements — optionally narrowed to one LOINC code or ca
fhir_get_patient_conditionsRead the Conditions recorded for one patient — the problem list — with their clinical and verification status
fhir_get_patient_encountersRead the Encounters for one patient — admissions, visits and consultations — with their class, period and the practitioners involved
fhir_get_patient_medicationsRead the MedicationRequests for one patient — what has been prescribed, in what dosage, by whom and with what status
fhir_get_patient_reportsRead the DiagnosticReports for one patient — laboratory panels, imaging reports and pathology — with their category, status and conclusions
fhir_get_patient_everythingRun the $everything operation on one patient: every resource the server associates with them, in one Bundle
fhir_next_pageFetch the next page of a search result

FAQ

Which Copilot is this for? Microsoft 365 Copilot at work, through agents built in Copilot Studio. The Microsoft Copilot app for personal accounts has no option to add your own MCP server.

What do I need? A work account with access to Copilot Studio (a license or a trial) to build the agent. People who use it in Microsoft 365 Copilot or Teams need access to the agent: share it with them, or ask an admin to publish it to the organization. If your organization applies data policies to Power Platform connectors, they cover MCP servers too.

The agent doesn't call the tools. Check that the header name is exactly X-API-Key and that the key belongs to the same MCP server as the URL, and make the server description specific: Copilot Studio uses it to decide when to call the server. Publish the agent again after each change; in an open chat, type "start over" to get the new version.

Next steps

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