Awesome Healthcare MCP Server

A curated list of healthcare Model Context Protocol (MCP) servers for clinical decision support, FHIR interoperability, revenue cycle management, medical research, and HIPAA-compliant AI workflows.

Every server is independently rated for HIPAA compliance (L1–L5) and clinical validity (A–D) by a board-certified physician.

Contents

• Trust Framework
• Revenue Cycle Management
• Clinical Decision Support
• FHIR and Health Data Interoperability
• Quality Compliance and Regulatory
• Life Sciences and Research
• Population Health and Value-Based Care
• Workflow Bundles

Trust Framework

Every MCP server listed here carries two independent ratings maintained by Ralph Martello, MD.

HIPAA Compliance Level

Badge	Level	Description
L5	HIPAA-Ready	Full BAA, AES-256, audit logging, RBAC, pen-tested
L4	HIPAA-Aware	Encryption in transit, no PHI storage, privacy-by-design
L3	De-identified Safe	Aggregate or de-identified data only
L2	Reference Only	Public data sources only (FDA, NLM, CMS)
L1	Unvetted	Not yet assessed

Clinical Validity Score

Badge	Score	Description
A	Clinically Validated	Evidence-based, peer-reviewed, physician-endorsed
B	Clinically Informed	Built with clinical input, follows guidelines
C	Operationally Useful	Administrative or financial tools, not clinical
D	Experimental	Research-stage, community-developed

All ratings are point-in-time architectural assessments, not certifications. See contributing.md for full rating criteria.

Revenue Cycle Management

• Healthcare Billing Codes - CPT, ICD-10, and HCPCS billing code lookup and search for revenue cycle workflows (L2 C Python).
• Medicaid MCP Server - Medicaid public data access including NADAC drug pricing (1.5M NDCs), Federal Upper Limits, state formularies, and drug rebate program data via data.medicaid.gov (L2 C JavaScript).
• Medicare MCP - CMS Medicare provider services, prescriber data, hospital utilization, drug spending, and Part B ASP pricing via the Socrata API with quarterly automated updates (L2 C JavaScript).
• ReimbursementEngine - Medicare coverage determination, ICD-10 coding, NPI validation, payer policy analysis, PubMed search, and bioRxiv/medRxiv preprint search across 18 tools (L4 C).

Clinical Decision Support

• BioThings MCP - Query genes, genetic variants, drugs, and taxonomic information via the BioThings API (L2 B Python).
• DrugBank MCP Server - Access 17,430+ drugs (13,166 small molecules, 4,264 biotech) with targets, enzymes, metabolic pathways, interactions, and regulatory data from the DrugBank Full Database (L2 B JavaScript).
• Evidence-Based Medicine MCP - Evidence-based medical advice MCP for clinical decision support workflows (L2 B TypeScript).
• FDA MCP Server - Comprehensive FDA pharmaceutical intelligence covering 47,000+ drug products, FAERS adverse events, drug recalls, Orange Book small-molecule approvals, and Purple Book biologics (L2 B JavaScript).
• Healthcare Data Hub - All-in-one server for FDA drug info, PubMed, medRxiv, NCBI Bookshelf, clinical trials, ICD-10, DICOM metadata, and medical calculator (L2 B Node.js).
• MCP-LOINC - LOINC API wrapper for medical terminology standardization and lab code lookup (L2 B Python).
• MedAdapt Content Server - AI-assisted medical learning with adaptive content from PubMed, NCBI Bookshelf, and user documents (L2 B Python).
• Medical-MCP - Comprehensive medical information from FDA, WHO, PubMed, RxNorm, and Google Scholar (L2 B Python).
• NCCN Guidelines MCP - NCCN cancer treatment guidelines access for oncology decision support (L2 A Python).
• NexOnco MCP - Oncology clinical evidence and precision medicine decision support (L2 B Python).
• NICE MCP Server - UK NICE Clinical Guidelines access for evidence-based clinical decision support (L2 A).
• Oncofiles - AI-powered medical document management for cancer patients and caregivers with OCR, lab value tracking with reference ranges, pre-cycle safety checks, and PubMed/ClinicalTrials.gov integration across 76 tools (L4 B Python).
• SNOMED CT MCP - SNOMED CT concept lookup via FHIR R4 terminology server for clinical coding (L2 A Python).

FHIR and Health Data Interoperability

• AEHRC FHIR Tools - FHIR tools by Australian e-Health Research Centre (CSIRO) for health data interoperability (L4 B TypeScript).
• AgentCare MCP - Healthcare tools and prompts for interacting with FHIR data and medical resources on EMRs like Cerner and Epic (L4 B TypeScript).
• AWS HealthLake MCP Server - MCP server for AWS HealthLake FHIR operations with 11 tools for FHIR resource management and automatic datastore discovery (L5 B Python).
• Azure FHIR MCP Server - Azure Health Data Services FHIR MCP server for cloud-native health data integration (L4 B Python).
• DICOM MCP Server - Query, read, and move medical images and reports from PACS and other DICOM-compliant systems (L3 B Python).
• EHR-MCP - Framework-agnostic SMART-on-FHIR interoperability layer for multi-agent healthcare AI, returning typed ClinicalContextBundle from Epic, Cerner, and any FHIR R4 EHR (L4 B Python).
• Flexpa FHIR MCP - Connect to health plans and retrieve patient claims, coverage, and clinical data via FHIR (L4 C TypeScript).
• Health Record MCP - Connect to an EHR and make clinical data available via MCP, by Josh Mandel of SMART Health IT (L4 A TypeScript).
• LangCare MCP FHIR - Enterprise-grade FHIR R4 proxy for AI agents with 40+ clinical skills, multi-EMR support (Epic, Cerner, GCP), and SMART-on-FHIR auth (L4 B Go).
• Medplum MCP Server - Official Medplum MCP proxy exposing FHIR resources from Medplum-hosted or self-hosted FHIR backends to AI agents (L4 B TypeScript).
• Momentum FHIR MCP Server - Natural language interface for healthcare data that eliminates weeks of FHIR learning and prevents LLM hallucination of medical codes (L4 B TypeScript).
• Orthanc DICOM MCP - DICOM MCP with Orthanc PACS integration, radiology report generation, FHIR ImagingStudy, and mini-RIS (L3 B Python).
• Quiquemz FHIR MCP - C# FHIR R4 MCP server with CRUD, search, transactions, and Azure FHIR Server support (L4 B C#).
• Secure FHIR MCP - HIPAA-hardened FHIR MCP with PHI masking, break-glass access, OWASP security, and audit logging (L4 B TypeScript).
• WSO2 FHIR MCP Server - Expose any FHIR server or API as an MCP server with SMART-on-FHIR authentication and full CRUD on FHIR resources (L4 B TypeScript).

Quality Compliance and Regulatory

• Innovaccer HMCP - Specialized MCP extension with HIPAA guardrails, OAuth2, audit trails, and compliance layer for enterprise healthcare AI (L5 C).
• OMOP MCP - OMOP concept mapping via LLMs by Mayo Clinic NLP group for clinical data standardization (L2 B Python).
• DataMimic - Deterministic synthetic healthcare test data generation for CI/CD and analytics, HIPAA-safe with MCP integration (L3 C Python).
• PyOMOP - OHDSI/OMOP clinical data management with FHIR import for observational research (L3 B Python).

Life Sciences and Research

• 3D Slicer MCP - Medical imaging integration via 3D Slicer for radiology and surgical planning workflows (L3 B).
• BioMCP - Clinical trials, genomics, PubMed, and variant annotation in Rust for biomedical research workflows (L2 B Rust).
• CDISC Library MCP - CDISC Library access for clinical data standards and regulatory submissions (L2 B JavaScript).
• ClinicalTrials.gov MCP - ClinicalTrials.gov REST API for searching and retrieving clinical trial data (L2 A TypeScript).
• GenePattern MCP - Official GenePattern server bridging AI assistants to 200+ peer-reviewed bioinformatics modules for gene expression, single-cell, and genomic analysis (L2 B Python).
• GenomeMCP - Clinical genomics intelligence via ClinVar, gnomAD, Reactome, and NCBI-BLAST with variant interpretation and population genetics for precision medicine workflows (L2 B Python).
• M3 MIMIC MCP - Query MIMIC-IV medical data via natural language for clinical research (L3 B Python).
• MCP Simple PubMed - Popular standalone PubMed MCP server for biomedical literature search (L2 A Python).
• Protein Structure Analyzer - Protein structure analysis via MCP for research and drug discovery workflows (L2 D).
• Standalone PubMed MCP - Standalone PubMed search server for biomedical literature access and citation retrieval (L2 A).
• Medical MCPs - 100+ unified tools across 14 biomedical APIs including Reactome, KEGG, UniProt, OMIM, ChEMBL, and OpenFDA (L2 B Python).
• Medical Research MCP Suite - Cross-database medical research intelligence unifying ClinicalTrials.gov, PubMed, and FDA with AI analysis (L2 B TypeScript).
• Precision Medicine MCP - Multi-omics precision medicine platform with genomics, spatial transcriptomics, imaging, and clinician-in-the-loop workflows (L3 B Python).
• PubMed MCP - Advanced PubMed search with citation export (BibTeX, APA, MLA), author search, journal analysis, and article comparison (L2 A Python).
• Reactome MCP - Official Reactome MCP server exposing 40+ tools for pathway search, enrichment analysis, ID mapping, species/disease annotation, and biological pathway data export (L2 B TypeScript).
• TealFlow MCP - Build Teal R Shiny clinical trial analysis apps with AI assistance (L2 B Python).

Population Health and Value-Based Care

• Apple Health MCP Server - Access exported Apple Health data with built-in analytics for consumer health and population health workflows (L3 D).
• Apple Health MCP - Query Apple Health data with SQL and natural language via DuckDB for consumer and population health workflows (L3 D TypeScript).
• Oura MCP Server - Oura Ring health intelligence with chronotype classification, personalized sleep-need detection, 7-day forecasts, and multi-signal illness detection with 1-2 day advance warning (L3 D Python).
• PopHIVE MCP Server - Yale PopHIVE population health data for community health analysis and value-based care (L3 B JavaScript).

Workflow Bundles

Pre-configured MCP stacks for common healthcare workflows.

• Denial Fighter - Analyze, appeal, and prevent claim denials with NCD/LCD lookup, ICD-10 validation, and clinical evidence search.
• Prior Auth Stack - CMS-0057 aligned prior authorization workflow with coverage determination and FHIR submission.
• Clinical Reference Kit - Point-of-care reference tools for clinicians including drug info, literature search, and genomics.
• FHIR Interop Suite - Complete FHIR integration toolkit for CMS-0057 and HTI-1 compliance.
• Compliance Suite - Quality reporting and regulatory compliance with Medicare policy monitoring and HIPAA guardrails.

Footnotes

Rating Methodology

All HIPAA compliance levels and clinical validity scores are point-in-time architectural assessments, not ongoing guarantees or HIPAA certifications. Organizations must conduct their own due diligence before deploying any MCP server in a clinical or production environment.

CMS-0057 and HTI-1

Several FHIR MCP servers in this list directly support compliance with CMS-0057-F (Interoperability and Prior Authorization) and HTI-1 (Health Data, Technology, and Interoperability) federal mandates effective 2026-2027.

Contributing

See contributing.md for how to submit a healthcare MCP server to this list.