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Start by locating the failure: the tool may be missing from the agent’s configuration, its server may not have started or be reachable, authentication or permission may have failed, the file may be unavailable or unsupported, or the tool call and result may be malformed. Check those layers in that order, using the exact error and the identity that runs the agent; repeatedly reconnecting services or changing unrelated permissions can obscure the cause.

1. Confirm the agent has the tool

First check the configuration the running agent actually receives, not just the tool definition in your codebase. For OpenAI API workflows, tools are configured through the tools parameter; in the Agents API, check agent.tools. Your application must also handle function calls and provide an execution environment when a tool requires one. In an SDK workflow, confirm the tool is attached to the agent or specialist expected to use it. See OpenAI’s Using tools.

For MCP, verify that the server is configured and registered before the agent runs. Microsoft Agent 365’s initialization process loads configured servers from the manifest, registers their tools, and configures authentication. See Microsoft Agent 365 tooling.

Compare discovery with filters

  • Inspect the actual discovered tool list. If an allowlist is enabled, compare the list without the filter, then restore only the exact tool names returned.
  • Check spelling and capitalization in allowed_tools. Microsoft Foundry documents incorrect names as a cause of missing tools.
  • Check the platform’s naming convention. Foundry MCP tool names can include a server-label prefix, so the callable name may differ from the unprefixed name you expected.

Foundry’s toolbox guidance distinguishes these symptoms: zero tools can result from absent or invalid connection credentials; missing OpenAPI tools can indicate a malformed specification; and an incomplete list can result from incorrect allowed-tool names. Use its MCP troubleshooting guidance to match the observed outcome rather than treating every empty list as the same problem.

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2. Diagnose server startup and reachability

If the tool is configured but unavailable, find out whether the server started and whether the process that runs the connection can reach it. OpenAI recommends checking the failed-turn event and, for stdio MCP servers, the process logs. Verify that the configured command and dependencies work in the execution environment, that an inline stdio configuration uses an existing absolute working directory, and that the endpoint is reachable from the connection’s actual origin. See OpenAI’s MCP connections guide.

Match the connection type to its network location

  • HTTP MCP: Determine whether the connection is reached from OpenAI’s service or runs in the user’s environment. A service-hosted connection cannot necessarily reach an endpoint available only on your computer or private network.
  • Environment-origin connection: Confirm that the executor has network access to the endpoint. A URL that works in a developer’s browser may not work from the executor.
  • stdio MCP: Check the command, arguments, dependencies, process logs, and working directory in the environment that launches the process.

These execution modes have different reachability requirements; changing credentials will not fix an endpoint that the executing environment cannot reach.

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3. Separate authentication, consent, and authorization

Once the server is reachable, check whether it accepted the credentials and whether the identity behind those credentials can access the requested resource. Preserve the precise HTTP status or protocol error: it narrows the likely failing layer.

Read the error before changing credentials

  • 401: The request is unauthenticated. Check that the token or headers are present, current, and associated with the right server.
  • 403: The request is forbidden. Authentication may have succeeded, but the identity may lack permission.
  • 424 mcp_server_startup_failed: OpenAI’s Agents API error guidance associates this with server startup failure; return to server configuration and credentials.
  • Foundry -32006: Foundry documents this as an OAuth consent requirement. Its troubleshooting table also describes 401 cases involving an expired token or wrong scope. Confirm the required scope in current documentation for that service.

These mappings are platform-specific, not universal protocol rules. Compare them with OpenAI’s Errors and recovery and Microsoft Foundry’s MCP troubleshooting guidance; do not transfer a scope or fix from one service to another.

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Check the identity that runs the request

A connected app is not automatically authorized to every file or system behind it. OpenAI Help Center advises checking access on the provider account or administrator-managed source, because connecting an app does not add permissions in that source system. For a published agent, check the runtime identity specifically: it may be a service account or delegated user different from the person who configured the agent. See Troubleshooting plugins & apps in ChatGPT.

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4. If the agent finds a file but cannot use it

A filename or file detail is not proof that the agent retrieved the content or that the connected feature can analyze it. Separate “file not found” from “file found, contents unusable” before changing settings.

  • File not found: Check the connected provider account, source permissions, workspace configuration, sync or index status, and whether the file is inside the configured sync scope.
  • File found but unusable: Check whether content retrieval succeeded, whether the file type is supported, and whether the connected feature supports the requested operation.
  • Content is available elsewhere: Where appropriate, use a supported export or transcript, but only if you are authorized to share it.

These checks follow OpenAI Help Center’s app troubleshooting guidance. Reconnecting may not correct a source permission, sync-scope, or format limitation.

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5. Inspect failed calls and malformed results

If the tool is listed and the server responds, inspect the request and response structure—not only the assistant’s explanation. A model can describe a call as failed even when the underlying cause is a missing result block or an invalid continuation.

Match every tool-use request with a result

Anthropic documents an error when a tool-use ID has no corresponding tool-result block. Return one result for every tool-use block, and place results before text in the user message. When continuing a request, preserve protected thinking blocks unchanged and append the tool result as documented. See Anthropic’s tool-use troubleshooting guide.

Use the error details to choose a recovery

On Microsoft Foundry’s toolbox endpoint, inspect whether the MCP response contains an error field and read its code. Its troubleshooting material distinguishes consent-required responses, expired or wrong-scope tokens, prefixed tool names, unsupported non-streaming calls, and transient server errors. Retry a transient tools/list server error after a few seconds, as Foundry advises; do not apply that retry to a permission or configuration error.

For OpenAI structured errors, inspect error.code, error.message, and error.param where supplied. The documented mappings include invalid input or configuration, authentication and permission failures, unavailable resources, MCP startup failures, and temporary service or overload errors. Correct invalid input before retrying; for a temporary outage, follow the platform’s recovery guidance and check saved work where relevant. See OpenAI Errors and recovery.

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Work through the failure in order

  1. Tool discovery: Confirm the tool is attached to the running agent and present in its discovered list; inspect allowlists and exact naming.
  2. Server and network: Check startup logs, endpoint reachability from the actual execution origin, and the command or dependencies for stdio.
  3. Authentication and access: Read the status or protocol code, validate the credential and scope, then check permissions for the runtime identity at the source.
  4. File retrieval and capability: Verify sync scope and content retrieval, then confirm the file type and requested operation are supported.
  5. Call and result structure: Match tool-use IDs to results, preserve required message structure, and follow the error’s platform-specific recovery.

Keep the original error code and message with the configuration and execution context that produced it. Tool discovery, server reachability, authorization, file retrieval, and transcript handling are separate failure layers; a fix in one does not establish that the others are working.

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