# Rethinking MCP Security: A Large-Scale Study of Runtime MCP Servers and Security Scanner Reliability

arXiv: https://arxiv.org/abs/2607.11086 · HTML: https://mlsanity.com/paper/2607.11086/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Placed in Agent threats, guardrails and governance, one of 16 directions in LLM agents and tool use.
- First posted on arXiv 13 Jul 2026.

## Placed in

- LLM agents and tool use / [Agent threats, guardrails and governance](https://mlsanity.com/agents/agent-threats-guardrails-and-governance/)

## Built on by (most cited first, 2 of 2)

- [What a Random Draw from the MCP Registry Contains, and What Tool-Use Benchmarks Contain Instead](https://mlsanity.com/paper/2609.10962/) (2026)
- [Attack Success Rate Is Not a Number: On Measurement Validity in Agentic AI Security Evaluation](https://mlsanity.com/paper/2609.25173/) (2026)

## Abstract (arXiv)

The Model Context Protocol (MCP) has rapidly established itself as a standard interface for enabling LLM-based agents to interact with external tools and services. As MCP servers are increasingly entrusted with security-sensitive operations, understanding their real-world risks has become critical. In practice, due to the absence of large-scale runtime MCP servers, such understanding largely relies on security scanners applied to a small number of cases, yet the reliability of these assessments remains unclear. In this study, we revisit how MCP security is measured. We present MCPZoo, the largest collection of MCP servers for dynamic analysis to date. MCPZoo is constructed through a multi-agent framework for transforming in-the-wild static repositories into dynamic services. The framework emulates how human experts build, diagnose, and iteratively repair deployment and runtime defects by combining environment inference with feedback-driven refinement. To ensure practical interactivity at runtime, the servers are validated via real protocol interactions. As a result, MCPZoo contains 64,611 unique MCP servers (113,927 in total), with more than 37,288 supporting dynamic analysis. Leveraging MCPZoo, we conduct the first ecosystem-scale measurement of MCP servers and the scanners that analyze them. While existing scanners report that 96.89% of servers are risky, we find that these signals are unreliable. In particular, manual validation shows that less than 50% of sampled alerts are true positives, and scanner outputs exhibit clear inconsistency across scanners. Overall, MCPZoo enables large-scale, reproducible measurement of MCP server security and exposes limitations of current scanning practices. We further release a public query interface to support practical risk assessment of MCP servers.