How to Use the ClinicalTrials.gov MCP in Claude Code

Q: How do I add the ClinicalTrials.gov MCP Server to Claude Code?

Run claude mcp add --transport http clinical-trials -- in your terminal. This command registers the server in your local /.claude.json configuration file.

Q: Can Claude Code filter trials by phase and sponsor?

Yes, the searchclinicaltrials tool supports filtering by trial phase, sponsor, and recruitment status. The agent applies these parameters based on your CLI instructions.

Pipe live ClinicalTrials.gov data, NCT details, and recruiting status directly into your terminal workflows with Claude Code.

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Connect ClinicalTrials.gov MCP to Claude Code

Create your Vinkius account to connect ClinicalTrials.gov to Claude Code and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

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Setup ClinicalTrials.gov with Claude Code

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Pipe clinical study data directly to shell tools

This MCP setup lets you query the registry without leaving your terminal. Claude Code runs `search_clinical_trials` to pull study data, allowing you to pipe the JSON output directly into jq, grep, or custom bash scripts. You can automate complex data gathering pipelines. The agent formats the output instantly, making it easy to feed clinical trial records into your backend databases.

Automate recruitment alerts with this MCP Server

Tracking open studies is trivial from the command line. Claude Code uses `find_recruiting_trials` to look for active enrollments and can write a cron job to alert you when new trials appear. You don't have to build a custom scraper. The agent handles the queries and writes the shell commands to monitor specific medical conditions automatically.

Fetch complete trial details by NCT identifier

Pulling down full trial protocols takes a single terminal command. Claude Code calls `get_trial_details` with the NCT ID and dumps the parsed eligibility rules and study arms straight to stdout. This eliminates the need for slow web browsers. You get raw, structured data instantly, ready to be saved as a markdown file or committed to a git repository.

Setup guide

Set up ClinicalTrials.gov MCP in Claude Code

Prerequisites

Claude Code CLI installed (npm install -g @anthropic-ai/claude-code)
Active Vinkius subscription with a valid endpoint token

1

Run the add command

Open your terminal and run the command shown on the right. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com. Use --scope user to make it available across all projects.
2

Verify the connection

Start a Claude Code session and type /mcp to list connected servers. You should see clinicaltrialsgov-mcp with a green status indicator.
3

Start using tools

Ask Claude Code something like "Check my latest ClinicalTrials.gov transactions." It will automatically discover and invoke the available ClinicalTrials.gov tools.

Terminal

claude mcp add --transport http clinicaltrialsgov-mcp https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

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Prerequisites

Claude Code CLI installed
Active Vinkius subscription with a valid endpoint token

1

Open the config file

Create or edit .mcp.json in your project root for project-level scope, or ~/.claude.json for user-level scope.
2

Add the ClinicalTrials.gov MCP

Paste the JSON snippet shown on the right into the mcpServers object. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Restart Claude Code

Start a new Claude Code session. Type /mcp to confirm the server is connected. The tools will be automatically available in your conversation.

.mcp.json

{
  "mcpServers": {
    "clinicaltrialsgov-mcp": {
      "type": "url",
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

Get your connection token →

Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by ClinicalTrials.gov. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about ClinicalTrials.gov MCP in Claude Code

You ask the CLI agent to find trials for a specific condition. The agent uses the MCP toolset to execute `search_clinical_trials` behind the scenes and prints the structured results directly to your terminal.

Yes, you can run Claude Code headlessly in your CI/CD environment. It uses the `search_clinical_trials` tool to fetch updates and can automatically commit the new data to your repo.

Run `claude mcp add --transport http clinical-trials -- ` in your terminal. This command registers the server in your local `~/.claude.json` configuration file.

Yes, the `search_clinical_trials` tool supports filtering by trial phase, sponsor, and recruitment status. The agent applies these parameters based on your CLI instructions.

All terminal queries, condition keywords, and NCT identifiers are sent through an isolated V8 sandbox. Vinkius does not store or monitor the medical terms you query, keeping your research pipeline secure.

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