ClinicalTrials.gov MCP Server

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Overview

Seven tools for searching, discovering, analyzing, and matching clinical trials:

Tools

clinicaltrials_search_studies

Primary search tool with full ClinicalTrials.gov query capabilities.

• Full-text and field-specific queries (condition, intervention, sponsor, location, title, outcome)
• Status and phase filters with typed enum values
• Geographic proximity filtering by coordinates and distance
• Advanced AREA[] Essie expression support for complex queries
• Field selection to reduce payload size (full records are ~70KB each)
• Pagination with cursor tokens, sorting by any field

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clinicaltrials_get_study_results

Fetch posted results data for completed studies.

• Outcome measures with statistics, adverse events, participant flow, baseline characteristics
• Section-level filtering (request only the data you need)
• Optional summary mode condenses full results (~200KB) to essential metadata (~5KB per study)
• Batch multiple NCT IDs per call with partial-success reporting
• Separate tracking of studies without results and fetch errors

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clinicaltrials_find_eligible

Match a patient profile to eligible recruiting trials.

• Takes age, sex, conditions, and location as patient demographics
• Builds optimized API queries with demographic filters (age range, sex, healthy volunteers)
• Re-ranks results so studies whose own condition matches a requested condition surface above tangential matches from the upstream fuzzy condition search
• Returns studies with eligibility and location fields for the caller to evaluate
• Provides actionable hints when no studies match (broaden conditions, adjust filters)

Features

Built on @cyanheads/mcp-ts-core:

• Declarative tool/resource/prompt definitions with Zod schemas and format functions
• Unified error handling — handlers throw, framework catches and classifies
• Dual transport: stdio and Streamable HTTP from the same codebase
• Pluggable auth (none, jwt, oauth) for HTTP transport
• Structured logging with optional OpenTelemetry tracing

ClinicalTrials.gov-specific:

• Type-safe client for the ClinicalTrials.gov REST API v2
• Public API — no authentication or API keys required
• Retry with exponential backoff (3 attempts) and rate limiting (~1 req/sec)
• HTML error detection and structured error factories

Getting Started

Public Hosted Instance

A public instance is available at https://clinicaltrials.caseyjhand.com/mcp — no installation required. Point any MCP client at it via Streamable HTTP:

{
  "mcpServers": {
    "clinicaltrialsgov-mcp-server": {
      "type": "streamable-http",
      "url": "https://clinicaltrials.caseyjhand.com/mcp"
    }
  }
}

Self-Hosted / Local

Add to your MCP client config (e.g., claude_desktop_config.json):

{
  "mcpServers": {
    "clinicaltrialsgov-mcp-server": {
      "type": "stdio",
      "command": "bunx",
      "args": ["clinicaltrialsgov-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio"
      }
    }
  }
}

Or for Streamable HTTP:

MCP_TRANSPORT_TYPE=http
MCP_HTTP_PORT=3010

Prerequisites

• Bun v1.3.0 or higher (or Node.js >= 24.0.0)

Installation

1. Clone the repository:

   git clone https://github.com/cyanheads/clinicaltrialsgov-mcp-server.git
   

2. Navigate into the directory:

   cd clinicaltrialsgov-mcp-server
   

3. Install dependencies:

   bun install
   

Configuration

All configuration is optional — the server works with defaults and no API keys.

Running the Server

Local Development

• Build and run the production version:

  bun run build
  bun run start:http   # or start:stdio
  

• Run checks and tests:

  bun run devcheck     # Lints, formats, type-checks
  bun run test         # Runs test suite
  

Docker

docker build -t clinicaltrialsgov-mcp-server .
docker run -p 3010:3010 clinicaltrialsgov-mcp-server

Project Structure

Development Guide

See CLAUDE.md for development guidelines and architectural rules. The short version:

• Handlers throw, framework catches — no try/catch in tool logic
• Use ctx.log for request-scoped logging, no console calls
• Register new tools and resources in the index.ts barrel files

Contributing

Issues and pull requests are welcome. Run checks before submitting:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.