GitHub - snyk/agent-scan: Security scanner for AI agents, MCP servers and agent skills.

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

Note: CLI output is experimental and subject to change

Agent Scan v0.5.x (planned for deprecation)

The raw output of this CLI — including issue codes, field names, severity labels, and response structure — is experimental and may change without notice between releases. We do not recommend building production workflows that depend on specific CLI output fields or issue codes.

Agent Scan v0.6 and later

The raw output of this CLI — including risk indicator names, scores, field names, and response structure — is experimental and may change without notice between releases. We do not recommend building production workflows that depend on specific CLI output fields or risk names.

If you are an enterprise customer using Snyk to manage agent security risk at scale, the CLI output may not reflect what is sent to and shown in the Evo platform. The underlying integration, discovery, and risk assessment that powers enterprise deployments is stable and supported — any changes will be communicated in line with standard Snyk product practices. Contact your account team for deployment guidance.

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 v0.5.x output

Agent Scan v0.6 and later output

Agent Scan helps you discover all your installed agent components (harnesses, MCP servers, and skills) and scans them for common threats like prompt injections, sensitive data handling, or malware payloads hidden in natural language. Ignore analysis on skills by using --no-skills.

Security Warning

⚠️ IMPORTANT: Scanning MCP configurations will execute the commands defined in them.

When Agent Scan scans an MCP configuration file, it starts the stdio MCP servers by executing the commands and arguments specified in the config. This is necessary to retrieve tool descriptions and perform security analysis.

Recommendations:

• Run scans inside a sandbox (Docker container, VM, or disposable environment) when evaluating untrusted or third-party MCP configs
• Review the consent prompt carefully during interactive scans, it shows the exact command and arguments that will be executed for each server
• Use --dangerously-run-mcp-servers only in trusted environments where you've verified all MCP server commands

By default, Agent Scan requires explicit user consent (y/n) before starting each stdio MCP server during interactive runs. This gives you control over what gets executed on your system.

Quick Start

Choose one of two ways to run Agent Scan:

1. Run the Python package with uvx using the instructions below.
2. Download a standalone binary for your platform from GitHub Releases. Releases also include the SBOM, checksums, signed checksums, and source code archives.

Before using either option:

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

Run with uvx

Have uv installed on your system. Choose the instructions for your CLI version.

Agent Scan v0.5.x

The examples pin v0.5.17 as a concrete v0.5.x release:

# Scan the whole machine
uvx snyk-agent-scan@0.5.17

# Scan a specific MCP configuration
uvx snyk-agent-scan@0.5.17 ~/.vscode/mcp.json

# Scan a single agent skill
uvx snyk-agent-scan@0.5.17 ~/path/to/my/SKILL.md

# Scan all Claude skills
uvx snyk-agent-scan@0.5.17 ~/.claude/skills

Agent Scan v0.6 and later

# Scan the whole machine
uvx snyk-agent-scan@latest

# Scan a specific MCP configuration
uvx snyk-agent-scan@latest ~/.vscode/mcp.json

# Scan a single agent skill
uvx snyk-agent-scan@latest ~/path/to/my/SKILL.md

# Scan all Claude skills
uvx snyk-agent-scan@latest ~/.claude/skills

v0.6 and later use the risk-based output and the 2026-07-10 analysis API.

Both versions scan MCP servers, tools, prompts, resources, and skills, and automatically discover supported agent configurations such as Claude Code/Desktop, Cursor, Gemini CLI, and Windsurf.

Run with a standalone binary

Download the binary for your operating system and architecture from the latest GitHub Release. The release page also provides an SBOM (sbom-<version>.json), checksum files, and GitHub-generated source code archives. See Verifying Standalone Binaries to verify your download.

Agent Scan v0.5.x example run

For the v0.6 risk-based output, see the v0.6 image at the top of this README.

Highlights

• Auto-discover MCP configurations, agent tools, skills
• Scanning of Claude, Cursor, Windsurf, Gemini CLI, Amp, Amazon Q, and other agents.

Agent Scan v0.5.x

• Detects 15+ distinct security risks across MCP servers and agent skills:
  • MCP: Prompt Injection, Tool Poisoning, Tool Shadowing, Toxic Flows
  • Skills: Prompt Injection, Malware Payloads, Untrusted Content, Credential Handling, Hardcoded Secrets

Agent Scan v0.6 and later

• Detects 15 distinct security risks across MCP servers and agent skills:
  • MCP: Prompt injection, dangerous words, untrusted content, private data, and destructive capabilities
  • Skills: prompt injection, suspicious downloads, malicious code, credential handling, secret detection, and more

Supported agents and capabilities

Agent Scan auto-discovers agents and their capabilities (MCP servers or skills) when their install paths exist. The table below shows on which operating systems each agent is scanned.

• ✓: at least one path is defined for that capability.
• ✗: the agent is listed for that OS but has no paths for that capability.
• —: that agent is not included for that OS.
• Skills Skills can be ignored by using --no-skills

Detection coverage by scope

The matrix above shows on which operating systems each agent is scanned. This one breaks detection down by configuration scope and component type (skills vs MCP servers), combined across operating systems. "Servers" means MCP servers.

The four scopes:

• System — machine-wide / admin-managed / enterprise config that applies to all users (e.g. managed-mcp.json, files under /etc, /Library/Application Support, or ProgramData).
• User — the user's home-directory config (applies across all their projects).
• Project / workspace — config scoped to an opened project or workspace.
• Extension / plugin — components bundled inside installed extensions or plugins.

Legend: ✓ detected · ✗ the agent supports this but Agent Scan does not scan it yet · N/A the agent has no such component at this scope.

† OpenClaw has no opened-project enumeration: its project/workspace skills are found only at the fixed ~/.openclaw/workspace/skills

‡ Amp stores project/workspace skills at .agents/skills (and the .claude/skills compatibility path); only the user-scope ~/.config/agents/skills is detected today, so project-scope skills are supported but not yet scanned.

Verifying Standalone Binaries

We use GPG signing on the release checksums file to ensure distribution integrity and authenticity.

Step-by-Step Verification Guide

1. Download the release assets: Download the binary for your platform (e.g., agent-scan-<version>-<os>-<arch>) and the signed checksums file (sha256sums.txt.asc) from the GitHub Releases page into the same directory.

2. Verify GPG signature of the checksums file: Download the GPG public key into the same directory, then run:

   gpg --import snyk-code-signing-public.pgp
   gpg --verify sha256sums.txt.asc

   Look for a line in the output saying gpg: Good signature from "Snyk Limited <code-signing@snyk.io>".

3. Verify the binary's integrity: After confirming the signature is valid, check that your downloaded binary matches the checksum:

   • On Linux (or macOS with coreutils):

     grep agent-scan-<version>-<os>-<arch> sha256sums.txt.asc | sha256sum -c -

   • On macOS (using default shasum):

     grep agent-scan-<version>-<os>-<arch> sha256sums.txt.asc | shasum -a 256 -c -

   This will output agent-scan-<version>-<os>-<arch>: OK.

Scanner Capabilities

Agent Scan v0.5.x

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 v0.6 and later

Agent Scan reports scored risk indicators for threats such as prompt injection, exposure to untrusted or private data, destructive capabilities, and malicious 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). 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.

Interactive Consent for MCP Servers

⚠️ Security Note: Scanning an MCP config executes the commands defined in it. Always review what will be executed before approving.

By default, Agent Scan prompts for user consent before starting each stdio MCP server during interactive runs. This consent flow:

• Shows the server name, command, and environment variables (redacted) that will be executed
• Allows you to approve or decline each server individually
• Prevents potentially untrusted servers from running without your explicit permission
• Records declined servers with a user_declined error (they are never started)

Best Practices:

• Review the command and arguments carefully before approving
• When scanning untrusted or third-party MCP configs, run Agent Scan inside a sandbox (Docker, VM, or disposable environment)
• Decline any servers with unfamiliar or suspicious commands

For non-interactive environments (e.g., CI/CD pipelines), you must use the --dangerously-run-mcp-servers flag to bypass the consent prompt and start all servers automatically. Only use this flag in trusted environments where all MCP server commands have been verified.

Analysis and Validation

Agent Scan validates discovered components with local checks and the Agent Scan API. It sends the component information needed for analysis, including agent application details, MCP server configurations and signatures, tool names and descriptions, and skill content. Secrets in configuration values and text are redacted before transmission.

By using Agent Scan, you agree to the Snyk terms of use for Agent Scan.

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

CLI Parameters

The complete flag reference is in docs/cli-reference.md. Most commands and flags are shared across v0.5.x and v0.6 and later.

Shared commands

snyk-agent-scan scan [CONFIG_FILE...]       Scan MCP servers and skills (default)
snyk-agent-scan inspect [CONFIG_FILE...]    Inspect components without analysis
snyk-agent-scan help                        Display help

Options shared by both version lines

These options exist in both v0.5.x and v0.6 and later. Their command applicability is detailed in the full CLI reference.

--storage-file FILE               Path to store scan state (default: ~/.mcp-scan)
--analysis-url URL                Analysis endpoint; the default API version depends on the CLI version
--verification-H HEADER           Additional analysis request header (repeatable)
--mcp-oauth-tokens-path PATH      OAuth tokens for protected remote MCP servers
--verbose                         Enable detailed logging
--print-errors                    Show error details and tracebacks
--print-full-descriptions         Show full entity descriptions without truncation
--json                            Emit JSON; the response schema depends on the CLI version
--skip-ssl-verify                 Disable TLS certificate verification
--skills / --no-skills            Include skills (default) or skip them
--scan-all-users                  Scan all readable user home directories
--show-analysis-results           Force synchronous analysis so results display for push-key scans
--ci                              Exit non-zero when findings or operational failures remain
--server-timeout SECONDS          MCP connection timeout (default: 10)
--suppress-mcpserver-io BOOL      Suppress stdio MCP server stderr
--dangerously-run-mcp-servers     Skip consent and start configured stdio MCP servers
--control-server URL              Upload destination (repeatable)
--control-server-H HEADER         Header for the current control-server block
--control-identifier ID           Identifier for the current control-server block
--no-bootstrap                    Accepted compatibility no-op; does not change behavior
--checks-per-server NUM           Accepted compatibility no-op; does not change behavior

Agent Scan v0.5.x

--analysis-url URL                Defaults to the 2025-09-02 analysis API
--ignore-issues-codes CODES       Comma-separated E/W security finding codes and X failure codes to ignore in CI

v0.5.x emits issue-code findings and path-keyed ScanPathResult JSON. See the v0.5.x CLI reference and issue-code reference.

Agent Scan v0.6 and later

--analysis-url URL                Defaults to the 2026-07-10 analysis API
--ignore-risks NAMES              Comma-separated risk names to omit from output and CI evaluation
--ignore-failure-codes CODES      Comma-separated X codes to omit from CI evaluation
--show-full-discovery             List every MCP entity and skill file instead of compact scan summaries

v0.6 and later emit scored risk indicators and scan_path_responses JSON. Human-readable scan output is compact by default; --show-full-discovery expands it without changing JSON or inspect output. See the v0.6-and-later CLI reference, risk reference, and failure-code reference.

Examples

# Scan all known MCP configs and agent skills
snyk-agent-scan

# Scan a specific config file or skill
snyk-agent-scan ~/custom/config.json
snyk-agent-scan ~/path/to/my/SKILL.md

# Inspect without security analysis
snyk-agent-scan inspect

# CI mode
snyk-agent-scan --ci --dangerously-run-mcp-servers

Demo

This repository includes a vulnerable MCP server that demonstrates Model Context Protocol security findings that Agent Scan reports.

How to demo MCP security findings?

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

3. Run the appropriate version:

   • Agent Scan v0.5.x (issue-code output): uvx --python 3.13 snyk-agent-scan@0.5.17 scan mcp.json
   • Agent Scan v0.6 and later (risk-based output): uvx --python 3.13 snyk-agent-scan@latest scan 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

• Documentation index — Versioned documentation for both CLI lines.
• CLI reference — v0.5.x and v0.6-and-later commands, flags, options, and environment variables.
• Scanning — v0.5.x and v0.6-and-later scanning behavior and examples.
• JSON output — The v0.5.x path-keyed output and the v0.6 response schema.
• Issue Codes — v0.5.x E* and W* security finding reference.
• Risk reference — v0.6 security risk indicators, scores, and evidence fields.
• Failure codes — v0.6 operational discovery, inspection, and analysis failures.

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.