Introducing FHIR MCP Server: Natural Language Interface for Healthcare Data

Developers building AI solutions in healthcare face a frustrating reality. FHIR is the gold standard for healthcare data exchange, but it comes with overwhelming complexity. Teams spend weeks learning FHIR specifications instead of building healthcare solutions. Even worse, when LLMs try to work with medical data, they hallucinate LOINC codes and create inaccurate clinical queries.

At Momentum, we believe healthcare AI should be accessible to every developer. That's why we're introducing the FHIR MCP Server, an open-source tool that eliminates FHIR complexity through natural language interfaces powered by the Model Context Protocol.

What is the Model Context Protocol

The Model Context Protocol (MCP) creates a universal standard for connecting AI agents with data sources and tools. Think of it as a bridge that lets any AI client communicate with any system through a common language. Claude Desktop, Cursor, CoPilot, and other popular AI tools already support MCP out of the box. This means developers can build once and connect to multiple AI clients, while AI agents get secure, standardized access to healthcare data without custom integrations.

Why Healthcare Needs MCP

Healthcare systems require more than generic data protocols. Medical data is highly sensitive, strictly regulated, and incredibly complex. Standard AI agents struggle with healthcare-specific challenges like FHIR resource relationships, medical terminology validation, and compliance requirements.

Electronic Health Records (EHRs) and clinical systems generate vast amounts of structured data, but accessing this information efficiently requires specialized knowledge of healthcare standards and protocols. Healthcare developers need tools that understand medical contexts, prevent clinical data errors, and maintain security standards. Generic solutions simply can't handle the precision healthcare demands.

FHIR MCP Server Offering

Momentum's FHIR MCP Server bridges this gap with three core capabilities built specifically for healthcare development.

• Complete FHIR Integration: The server provides full CRUD operations for all major FHIR resources through dedicated tools. Developers get specialized modules for Patient, Observation, Condition, Medication, and other critical resources, plus a generic tool for any FHIR resource type.
• Intelligent Medical Terminology: Built-in LOINC integration automatically translates natural language queries into precise FHIR requests. When you ask "Has the patient had a lipid profile in the last year?", the system automatically finds the correct LOINC codes and generates accurate FHIR queries.
• Smart Document Processing: The RAG-enabled pipeline handles medical documents in multiple formats including TXT, PDF, CSV, and JSON. Documents are intelligently chunked and stored as vector embeddings in Pinecone, enabling semantic search across all patient documents without processing entire files.

FHIR MCP Server in Action

Consider a doctor reviewing a patient who complains of headaches. Instead of manually searching through patient history, they can simply ask in natural language whether any previously diagnosed conditions might be related to current symptoms.

The FHIR MCP Server automatically retrieves relevant patient conditions, analyzes medication history, checks recent lab results, and provides a comprehensive clinical picture. All through simple conversation with an AI assistant.

For healthcare developers, this means building clinical decision support systems that actually help doctors instead of creating more administrative burden.

Get Started with FHIR MCP Server

Whether you're building AI-powered clinical tools or need to integrate FHIR data into existing systems, FHIR MCP Server is production-ready and open source.

• Complete documentation, setup guides, and examples are available at github.com/the-momentum/fhir-mcp-server
• Watch our demos showing real patient data analysis and clinical workflows
• Configure with Claude Desktop, Cursor, or any MCP-compatible client in under five minutes
• Use the comprehensive SDK to create healthcare-specific AI agents that understand medical contexts
• Curious how to use this MCP server with custom agents built using LlamaIndex? Check out this GitHub Gist for step-by-step implementation

Healthcare development should focus on patient outcomes, not wrestling with data formats. With FHIR MCP Server, we're making that vision reality for every healthcare developer.