Snyk Agent Scan

Snyk Agent Scan

Discover and scan agent components on your machine for prompt injections
and vulnerabilities (including agents, MCP servers, skills).

NEW Read our technical report on the emerging threats of the agent skill eco-system published together with Agent Scan 0.4, which adds support for scanning agent skills.

Agent Scan helps you keep an inventory of all your installed agent components (harnesses, MCP servers, skills) and scans them for common threats like prompt injections, sensitive data handling, or malware payloads hidden in natural language.

Highlights

• Auto-discover MCP configurations, agent tools, skills
• Scanning of Claude, Cursor, Windsurf, Gemini CLI, and other agents.
• Detects 15+ distinct security risks across MCP servers and agent skills:
  • MCP: Prompt Injection, Tool Poisoning, Tool Shadowing, Toxic Flows, Rug Pull
  • Skills: Prompt Injection, Malware Payloads, Untrusted Content, Credential Handling, Hardcoded Secrets

Quick Start

To get started:

1. Sign up at Snyk and get an API token from https://app.snyk.io/account (API Token → KEY → click to show).
2. Set the token as an environment variable before running any scan:

   export SNYK_TOKEN=your-api-token-here
   

3. Have uv installed on your system.

Scanning

To run a full scan of your machine (auto-discovers agents, MCP servers, skills), run:

uvx snyk-agent-scan@latest --skills

This will scan for security vulnerabilities in servers, skills, tools, prompts, and resources. It will automatically discover a variety of agent configurations, including Claude Code/Desktop, Cursor, Gemini CLI, and Windsurf. Omit --skills to skip skill analysis.

You can also scan particular configuration files:

# scan mcp configurations
uvx snyk-agent-scan@latest ~/.vscode/mcp.json
# scan a single agent skill
uvx snyk-agent-scan@latest --skills ~/path/to/my/SKILL.md
# scan all claude skills
uvx snyk-agent-scan@latest --skills ~/.claude/skills

Example Run

Scanner Capabilities

Agent Scan is a security scanning tool to both scan and inspect the supply chain of agent components on your machine. It scans for common security vulnerabilities like prompt injections, tool poisoning, toxic flows, or vulnerabilities in agent skills.

Agent Scan operates in two main modes which can be used jointly or separately:

1. Scan Mode: The CLI command snyk-agent-scan scans the current machine for agents and agent components such as skills and MCP servers. Upon completion, it will output a comprehensive report for the user to review.

2. Background Mode (MDM, Crowdstrike). Agent Scan scans the machine in regular intervals in the background, and reports the results to a Snyk Evo instance. This can be used by security teams to monitor the company-wide agent supply chain in a central location. To set this up, please contact us.

How It Works

Scanning

Agent Scan searches through your local agent's configuration files to find agents, skills, and MCP servers. For MCP, it connects to servers and retrieves tool descriptions.

It then validates the components, both with local checks and by invoking the Agent Scan API. For this, skills, agent applications, tool names, and descriptions are shared with Snyk. By using Agent Scan, you agree to the Snyk terms of use for Agent Scan.

A unique, persistent, and anonymous ID is assigned to your scans for analysis. You can opt out of sending this information using the --opt-out flag.

Agent Scan does not store or log any usage data, i.e. the contents and results of your MCP tool calls.

CLI Parameters

Agent Scan provides the following commands:

snyk-agent-scan - Security scanner for agents, MCP servers, and skills

Common Options

These options are available for all commands:

--storage-file FILE    Path to store scan results and scanner state (default: ~/.mcp-scan)
--base-url URL         Base URL for the verification server
--verbose              Enable detailed logging output
--print-errors         Show error details and tracebacks
--full-toxic-flows     Show all tools that could take part in toxic flow. By default only the top 3 are shown.
--json                 Output results in JSON format instead of rich text

Commands

scan (default)

Scan MCP configurations for security vulnerabilities in tools, prompts, and resources.

snyk-agent-scan scan [CONFIG_FILE...]

Options:

--checks-per-server NUM           Number of checks to perform on each server (default: 1)
--server-timeout SECONDS          Seconds to wait before timing out server connections (default: 10)
--suppress-mcpserver-io BOOL      Suppress stdout/stderr from MCP servers (default: True)
--skills                          Autodetects and analyzes skills
--skills PATH_TO_SKILL_MD_FILE    Analyzes the specific skill
--skills PATHS_TO_DIRECTORY       Recursively detects and analyzes all skills in the directory

inspect

Print descriptions of tools, prompts, and resources without verification.

snyk-agent-scan inspect [CONFIG_FILE...]

Options:

--server-timeout SECONDS      Seconds to wait before timing out server connections (default: 10)
--suppress-mcpserver-io BOOL  Suppress stdout/stderr from MCP servers (default: True)

help

Display detailed help information and examples.

snyk-agent-scan help

Examples

# Scan all known MCP configs
snyk-agent-scan

# Scan a specific config file
snyk-agent-scan ~/custom/config.json

# Just inspect tools without verification
snyk-agent-scan inspect

Demo

This repository includes a vulnerable MCP server that can demonstrate Model Context Protocol security issues that Agent Scan finds.

How to demo MCP security issues?

1. Clone this repository
2. Create an mcp.json config file in the cloned git repository root directory with the following contents:

{
  "mcpServers": {
    "Demo MCP Server": {
      "type": "stdio",
      "command": "uv",
      "args": ["run", "mcp", "run", "demoserver/server.py"],
    },
  },
}

3. Run Agent Scan: uvx --python 3.13 snyk-agent-scan@latest scan --full-toxic-flows mcp.json

Note: if you place the mcp.json configuration filepath elsewhere then adjust the args path inside the MCP server configuration to reflect the path to the MCP Server (demoserver/server.py) as well as the uvx command that runs Agent Scan with the correct filepath to mcp.json.

Agent Scan is closed to contributions

Agent Scan does not accept external contributions at this time.

We welcome suggestions, bug reports, or feature requests as GitHub issues.

Development Setup

To run Agent Scan from source, follow these steps:

uv run pip install -e .
uv run -m src.agent_scan.cli

Including Agent Scan results in your own project / registry

If you want to include Agent Scan results in your own project or registry, please reach out. There are designated APIs for this purpose. Using the standard Agent Scan API for large scale scanning is considered abuse and will result in your account being blocked.

Documentation

• Scanning — How scanning works, CLI parameters, and usage examples.
• Issue Codes — Reference for all security issues detected by Agent Scan.

Further Reading

• Introducing MCP-Scan
• MCP Security Notification Tool Poisoning Attacks
• WhatsApp MCP Exploited
• MCP Prompt Injection
• Toxic Flow Analysis
• Skills Report

Changelog

See CHANGELOG.md.