The rapid proliferation of Model Context Protocol (MCP)-based agentic systems has introduced a new category of security threats that existing frameworks are inadequately equipped to address. We present MCPThreatHive, an open-source platform that automates the end-to-end lifecycle of MCP threat intelligence: from continuous, multi-source data collection through AI-driven threat extraction and classification, to structured knowledge graph storage and interactive visualization. The platform operationalizes the MCP-38 threat taxonomy, a curated set of 38 MCP-specific threat patterns mapped to STRIDE, OWASP Top 10 for LLM Applications, and OWASP Top 10 for Agentic Applications. A composite risk scoring model provides quantitative prioritization. Through a comparative analysis of representative existing MCP security tools, we identify three critical coverage gaps that MCPThreatHive addresses: incomplete compositional attack modeling, absence of continuous threat intelligence, and lack of unified multi-framework classification.
Figures & tables
Figure 1: MCP three-tier architecture. The Host embeds an LLM and one or more MCP Clients, each maintaining a stateful session with an MCP Server over JSON-RPC 2.0.
Figure 2: MCPThreatHive four-stage pipeline architecture. Data flows left to right: intelligence sources feed into collection, items are classified by an LLM, results are stored in a relational database and knowledge graph, and exposed through interactive visualization and risk planning interfaces.
The Model Context Protocol (MCP) introduces a structurally distinct attack surface that existing threat frameworks, designed for traditional software systems or generic LLM deployments, do not adequately cover. This paper presents MCP-38, a protocol-specific threat taxonomy consisting of 38 threat categories (MCP-01 through MCP-38). The taxonomy was derived through a systematic four-phase methodology: protocol decomposition, multi-framework cross-mapping, real-world incident synthesis, and remediation-surface categorization. Each category is mapped to STRIDE, OWASP Top 10 for LLM Applications (2025, LLM01--LLM10), and the OWASP Top 10 for Agentic Applications (2026, ASI01--ASI10). MCP-38 addresses critical threats arising from MCP's semantic attack surface (tool description poisoning, indirect prompt injection, parasitic tool chaining, and dynamic trust violations), none of which are adequately captured by prior work. MCP-38 provides the definitional and empirical foundation for automated threat intelligence platforms.
The Model Context Protocol (MCP), introduced by Anthropic in November 2024 and now governed by the Linux Foundation's Agentic AI Foundation, has rapidly become the de facto standard for connecting large language model (LLM)-based agents to external tools and data sources, with over 97 million monthly SDK downloads and more than 177000 registered tools. However, this explosive adoption has exposed a critical gap: the absence of a unified, formal security framework capable of systematically characterizing, analyzing, and mitigating the diverse threats facing MCP-based agent ecosystems. Existing security research remains fragmented across individual attack papers, isolated benchmarks, and point defense mechanisms. This paper presents MCPSHIELD, a comprehensive formal security framework for MCP-based AI agents. We make four principal contributions: (1) a hierarchical threat taxonomy comprising 7 threat categories and 23 distinct attack vectors organized across four attack surfaces, grounded in the analysis of over 177000 MCP tools; (2) a formal verification model based on labeled transition systems with trust boundary annotations that enables static and runtime analysis of MCP tool interaction chains; (3) a systematic comparative evaluation of 12 existing defense mechanisms, identifying coverage gaps across our threat taxonomy; and (4) a defense in depth reference architecture integrating capability based access control, cryptographic tool attestation, information flow tracking, and runtime policy enforcement. Our analysis reveals that no existing single defense covers more than 34 percent of the identified threat landscape, whereas MCPSHIELD's integrated architecture achieves theoretical coverage of 91 percent. We further identify seven open research challenges that must be addressed to secure the next generation of agentic AI systems.
Nirajan Acharya, Gaurav Kumar Gupta
University of the Cumberlands · Youngstown State University
Model Context Protocol (MCP) servers have rapidly emerged over the past year as a widely adopted way to enable Large Language Model (LLM) agents to access dynamic, real-world tools. As MCP servers proliferate and become easy to adopt via open-source releases, understanding their security risks becomes essential for dependable production agent deployments. Recent work has developed MCP threat taxonomies, proposed mitigations, and demonstrated practical attacks. However, to the best of our knowledge, no prior study has conducted a systematic, large-scale assessment of weaknesses in open-source MCP servers. Motivated by this gap, we apply static code analysis to identify Common Weakness Enumeration (CWE) weaknesses and map them to common attack patterns and threat categories using the MITRE Common Attack Pattern Enumerations and Classifications (CAPEC) to ground risk in real-world threats. We then introduce a risk-assessment framework for the MCP landscape that combines these threats using a multi-metric scoring of likelihood and impact. Our findings show that many open-source MCP servers contain exploitable weaknesses that can compromise confidentiality, integrity, and availability, underscoring the need for secure-by-design MCP server development.
Pratyay Kumar, Miguel Antonio Guirao Aguilera, Srikathyayani Srikanteswara +2
New Mexico State University · GenAI and ML Research Visionary · University of Hartford