To use application permissions with your own API (as opposed to Microsoft Graph), you must first [expose the API](howto-add-app-roles-in-azure-ad-apps.md) by defining scopes in the API's app registration in the Azure portal. Then, [configure access to the API](howto-add-app-roles-in-azure-ad-apps.md#assign-app-roles-to-applications) by selecting those permissions in your client application's app registration. If you haven't exposed any scopes in your API's app registration, you won't be able to specify application permissions to that API in your client application's app registration in the Azure portal.
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