Connect to external tools with MCP

The Model Context Protocol (MCP) is an open standard for connecting AI agents to external tools and data sources. With MCP, your agent can query databases, integrate with APIs like Slack and GitHub, and connect to other services without writing custom tool implementations. MCP servers can run as local processes, connect over HTTP, or execute directly within your SDK application.

Quickstart

This example connects to the Claude Code documentation MCP server using HTTP transport and uses allowedTools with a wildcard to permit all tools from the server.

import { query } from "@anthropic-ai/claude-agent-sdk";

for await (const message of query({
  prompt: "Use the docs MCP server to explain what hooks are in Claude Code",
  options: {
    mcpServers: {
      "claude-code-docs": {
        type: "http",
        url: "https://code.claude.com/docs/mcp"
      }
    },
    allowedTools: ["mcp__claude-code-docs__*"]
  }
})) {
  if (message.type === "result" && message.subtype === "success") {
    console.log(message.result);
  }
}

The agent connects to the documentation server, searches for information about hooks, and returns the results.

Add an MCP server

You can configure MCP servers in code when calling query(), or in a .mcp.json file loaded via settingSources.

In code

Pass MCP servers directly in the mcpServers option:

import { query } from "@anthropic-ai/claude-agent-sdk";

for await (const message of query({
  prompt: "List files in my project",
  options: {
    mcpServers: {
      filesystem: {
        command: "npx",
        args: ["-y", "@modelcontextprotocol/server-filesystem", "/Users/me/projects"]
      }
    },
    allowedTools: ["mcp__filesystem__*"]
  }
})) {
  if (message.type === "result" && message.subtype === "success") {
    console.log(message.result);
  }
}

From a config file

Create a .mcp.json file at your project root. The SDK does not load filesystem settings by default, so set settingSources: ["project"] (Python: setting_sources=["project"]) in your options for the file to be picked up:

{
  "mcpServers": {
    "filesystem": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-filesystem", "/Users/me/projects"]
    }
  }
}

Allow MCP tools

MCP tools require explicit permission before Claude can use them. Without permission, Claude will see that tools are available but won’t be able to call them.

Tool naming convention

MCP tools follow the naming pattern mcp__<server-name>__<tool-name>. For example, a GitHub server named "github" with a list_issues tool becomes mcp__github__list_issues.

Grant access with allowedTools

Use allowedTools to specify which MCP tools Claude can use:

const _ = {
  options: {
    mcpServers: {
      // your servers
    },
    allowedTools: [
      "mcp__github__*", // All tools from the github server
      "mcp__db__query", // Only the query tool from db server
      "mcp__slack__send_message" // Only send_message from slack server
    ]
  }
};

Wildcards (*) let you allow all tools from a server without listing each one individually.

Prefer allowedTools over permission modes for MCP access. permissionMode: "acceptEdits" does not auto-approve MCP tools (only file edits and filesystem Bash commands). permissionMode: "bypassPermissions" does auto-approve MCP tools but also disables all other safety prompts, which is broader than necessary. A wildcard in allowedTools grants exactly the MCP server you want and nothing more. See Permission modes for a full comparison.

Discover available tools

To see what tools an MCP server provides, check the server’s documentation or connect to the server and inspect the system init message:

for await (const message of query({ prompt: "...", options })) {
  if (message.type === "system" && message.subtype === "init") {
    console.log("Available MCP tools:", message.mcp_servers);
  }
}

Transport types

MCP servers communicate with your agent using different transport protocols. Check the server’s documentation to see which transport it supports:

If the docs give you a command to run (like npx @modelcontextprotocol/server-github), use stdio
If the docs give you a URL, use HTTP or SSE
If you’re building your own tools in code, use an SDK MCP server

stdio servers

Local processes that communicate via stdin/stdout. Use this for MCP servers you run on the same machine:

In code
.mcp.json

const _ = {
  options: {
    mcpServers: {
      github: {
        command: "npx",
        args: ["-y", "@modelcontextprotocol/server-github"],
        env: {
          GITHUB_TOKEN: process.env.GITHUB_TOKEN
        }
      }
    },
    allowedTools: ["mcp__github__list_issues", "mcp__github__search_issues"]
  }
};

{
  "mcpServers": {
    "github": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_TOKEN": "${GITHUB_TOKEN}"
      }
    }
  }
}

HTTP/SSE servers

Use HTTP or SSE for cloud-hosted MCP servers and remote APIs:

In code
.mcp.json

const _ = {
  options: {
    mcpServers: {
      "remote-api": {
        type: "sse",
        url: "https://api.example.com/mcp/sse",
        headers: {
          Authorization: `Bearer ${process.env.API_TOKEN}`
        }
      }
    },
    allowedTools: ["mcp__remote-api__*"]
  }
};

{
  "mcpServers": {
    "remote-api": {
      "type": "sse",
      "url": "https://api.example.com/mcp/sse",
      "headers": {
        "Authorization": "Bearer ${API_TOKEN}"
      }
    }
  }
}

For HTTP (non-streaming), use "type": "http" instead.

SDK MCP servers

Define custom tools directly in your application code instead of running a separate server process. See the custom tools guide for implementation details.

MCP tool search

When you have many MCP tools configured, tool definitions can consume a significant portion of your context window. Tool search solves this by withholding tool definitions from context and loading only the ones Claude needs for each turn. Tool search is enabled by default. See Tool search for configuration options and details. For more detail, including best practices and using tool search with custom SDK tools, see the tool search guide.

Authentication

Most MCP servers require authentication to access external services. Pass credentials through environment variables in the server configuration.

Pass credentials via environment variables

Use the env field to pass API keys, tokens, and other credentials to the MCP server:

In code
.mcp.json

const _ = {
  options: {
    mcpServers: {
      github: {
        command: "npx",
        args: ["-y", "@modelcontextprotocol/server-github"],
        env: {
          GITHUB_TOKEN: process.env.GITHUB_TOKEN
        }
      }
    },
    allowedTools: ["mcp__github__list_issues"]
  }
};

{
  "mcpServers": {
    "github": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_TOKEN": "${GITHUB_TOKEN}"
      }
    }
  }
}

The ${GITHUB_TOKEN} syntax expands environment variables at runtime.

See List issues from a repository for a complete working example with debug logging.

HTTP headers for remote servers

For HTTP and SSE servers, pass authentication headers directly in the server configuration:

In code
.mcp.json

const _ = {
  options: {
    mcpServers: {
      "secure-api": {
        type: "http",
        url: "https://api.example.com/mcp",
        headers: {
          Authorization: `Bearer ${process.env.API_TOKEN}`
        }
      }
    },
    allowedTools: ["mcp__secure-api__*"]
  }
};

{
  "mcpServers": {
    "secure-api": {
      "type": "http",
      "url": "https://api.example.com/mcp",
      "headers": {
        "Authorization": "Bearer ${API_TOKEN}"
      }
    }
  }
}

The ${API_TOKEN} syntax expands environment variables at runtime.

OAuth2 authentication

The MCP specification supports OAuth 2.1 for authorization. The SDK doesn’t handle OAuth flows automatically, but you can pass access tokens via headers after completing the OAuth flow in your application:

// After completing OAuth flow in your app
const accessToken = await getAccessTokenFromOAuthFlow();

const options = {
  mcpServers: {
    "oauth-api": {
      type: "http",
      url: "https://api.example.com/mcp",
      headers: {
        Authorization: `Bearer ${accessToken}`
      }
    }
  },
  allowedTools: ["mcp__oauth-api__*"]
};

Examples

List issues from a repository

This example connects to the GitHub MCP server to list recent issues. The example includes debug logging to verify the MCP connection and tool calls. Before running, create a GitHub personal access token with repo scope and set it as an environment variable:

export GITHUB_TOKEN=ghp_xxxxxxxxxxxxxxxxxxxx

import { query } from "@anthropic-ai/claude-agent-sdk";

for await (const message of query({
  prompt: "List the 3 most recent issues in anthropics/claude-code",
  options: {
    mcpServers: {
      github: {
        command: "npx",
        args: ["-y", "@modelcontextprotocol/server-github"],
        env: {
          GITHUB_TOKEN: process.env.GITHUB_TOKEN
        }
      }
    },
    allowedTools: ["mcp__github__list_issues"]
  }
})) {
  // Verify MCP server connected successfully
  if (message.type === "system" && message.subtype === "init") {
    console.log("MCP servers:", message.mcp_servers);
  }

  // Log when Claude calls an MCP tool
  if (message.type === "assistant") {
    for (const block of message.message.content) {
      if (block.type === "tool_use" && block.name.startsWith("mcp__")) {
        console.log("MCP tool called:", block.name);
      }
    }
  }

  // Print the final result
  if (message.type === "result" && message.subtype === "success") {
    console.log(message.result);
  }
}

Query a database

This example uses the Postgres MCP server to query a database. The connection string is passed as an argument to the server. The agent automatically discovers the database schema, writes the SQL query, and returns the results:

import { query } from "@anthropic-ai/claude-agent-sdk";

// Connection string from environment variable
const connectionString = process.env.DATABASE_URL;

for await (const message of query({
  // Natural language query - Claude writes the SQL
  prompt: "How many users signed up last week? Break it down by day.",
  options: {
    mcpServers: {
      postgres: {
        command: "npx",
        // Pass connection string as argument to the server
        args: ["-y", "@modelcontextprotocol/server-postgres", connectionString]
      }
    },
    // Allow only read queries, not writes
    allowedTools: ["mcp__postgres__query"]
  }
})) {
  if (message.type === "result" && message.subtype === "success") {
    console.log(message.result);
  }
}

Error handling

MCP servers can fail to connect for various reasons: the server process might not be installed, credentials might be invalid, or a remote server might be unreachable. The SDK emits a system message with subtype init at the start of each query. This message includes the connection status for each MCP server. Check the status field to detect connection failures before the agent starts working:

import { query } from "@anthropic-ai/claude-agent-sdk";

for await (const message of query({
  prompt: "Process data",
  options: {
    mcpServers: {
      "data-processor": dataServer
    }
  }
})) {
  if (message.type === "system" && message.subtype === "init") {
    const failedServers = message.mcp_servers.filter((s) => s.status !== "connected");

    if (failedServers.length > 0) {
      console.warn("Failed to connect:", failedServers);
    }
  }

  if (message.type === "result" && message.subtype === "error_during_execution") {
    console.error("Execution failed");
  }
}

Troubleshooting

Server shows “failed” status

Check the init message to see which servers failed to connect:

if (message.type === "system" && message.subtype === "init") {
  for (const server of message.mcp_servers) {
    if (server.status === "failed") {
      console.error(`Server ${server.name} failed to connect`);
    }
  }
}

Common causes:

Missing environment variables: Ensure required tokens and credentials are set. For stdio servers, check the env field matches what the server expects.
Server not installed: For npx commands, verify the package exists and Node.js is in your PATH.
Invalid connection string: For database servers, verify the connection string format and that the database is accessible.
Network issues: For remote HTTP/SSE servers, check the URL is reachable and any firewalls allow the connection.

Tools not being called

If Claude sees tools but doesn’t use them, check that you’ve granted permission with allowedTools:

const _ = {
  options: {
    mcpServers: {
      // your servers
    },
    allowedTools: ["mcp__servername__*"] // Required for Claude to use the tools
  }
};

Connection timeouts

The MCP SDK has a default timeout of 60 seconds for server connections. If your server takes longer to start, the connection will fail. For servers that need more startup time, consider:

Using a lighter-weight server if available
Pre-warming the server before starting your agent
Checking server logs for slow initialization causes

Custom tools guide: Build your own MCP server that runs in-process with your SDK application
Permissions: Control which MCP tools your agent can use with allowedTools and disallowedTools
TypeScript SDK reference: Full API reference including MCP configuration options
Python SDK reference: Full API reference including MCP configuration options
MCP server directory: Browse available MCP servers for databases, APIs, and more

Agent SDK

Core concepts

Input and output

Extend with tools

Customize behavior

Control and observability

Deployment

SDK references

Connect to external tools with MCP

Quickstart

Add an MCP server

In code

From a config file

Allow MCP tools

Tool naming convention

Grant access with allowedTools

Discover available tools

Transport types

stdio servers

HTTP/SSE servers

SDK MCP servers

MCP tool search

Authentication

Pass credentials via environment variables

HTTP headers for remote servers

OAuth2 authentication

Examples

List issues from a repository

Query a database

Error handling

Troubleshooting

Server shows “failed” status

Tools not being called

Connection timeouts

Agent SDK

Core concepts

Input and output

Extend with tools

Customize behavior

Control and observability

Deployment

SDK references

​Quickstart

​Add an MCP server

​In code

​From a config file

​Allow MCP tools

​Tool naming convention

​Grant access with allowedTools

​Discover available tools

​Transport types

​stdio servers

​HTTP/SSE servers

​SDK MCP servers

​MCP tool search

​Authentication

​Pass credentials via environment variables

​HTTP headers for remote servers

​OAuth2 authentication

​Examples

​List issues from a repository

​Query a database

​Error handling

​Troubleshooting

​Server shows “failed” status

​Tools not being called

​Connection timeouts

​Related resources

Quickstart

Add an MCP server

In code

From a config file

Allow MCP tools

Tool naming convention

Grant access with allowedTools

Discover available tools

Transport types

stdio servers

HTTP/SSE servers

SDK MCP servers

MCP tool search

Authentication

Pass credentials via environment variables

HTTP headers for remote servers

OAuth2 authentication

Examples

List issues from a repository

Query a database

Error handling

Troubleshooting

Server shows “failed” status

Tools not being called

Connection timeouts

Related resources