diff --git a/e2e-tests/test_structured_output.py b/e2e-tests/test_structured_output.py
new file mode 100644
index 00000000..32e7ba21
--- /dev/null
+++ b/e2e-tests/test_structured_output.py
@@ -0,0 +1,204 @@
+"""End-to-end tests for structured output with real Claude API calls.
+
+These tests verify that the output_schema feature works correctly by making
+actual API calls to Claude with JSON Schema validation.
+"""
+
+import tempfile
+
+import pytest
+
+from claude_agent_sdk import (
+    ClaudeAgentOptions,
+    ResultMessage,
+    query,
+)
+
+
+@pytest.mark.e2e
+@pytest.mark.asyncio
+async def test_simple_structured_output():
+    """Test structured output with file counting requiring tool use."""
+
+    # Define schema for file analysis
+    schema = {
+        "type": "object",
+        "properties": {
+            "file_count": {"type": "number"},
+            "has_tests": {"type": "boolean"},
+            "test_file_count": {"type": "number"},
+        },
+        "required": ["file_count", "has_tests"],
+    }
+
+    options = ClaudeAgentOptions(
+        output_format={"type": "json_schema", "schema": schema},
+        permission_mode="acceptEdits",
+        cwd=".",  # Use current directory
+    )
+
+    # Agent must use Glob/Bash to count files
+    result_message = None
+    async for message in query(
+        prompt="Count how many Python files are in src/claude_agent_sdk/ and check if there are any test files. Use tools to explore the filesystem.",
+        options=options,
+    ):
+        if isinstance(message, ResultMessage):
+            result_message = message
+
+    # Verify result
+    assert result_message is not None, "No result message received"
+    assert not result_message.is_error, f"Query failed: {result_message.result}"
+    assert result_message.subtype == "success"
+
+    # Verify structured output is present and valid
+    assert result_message.structured_output is not None, "No structured output in result"
+    assert "file_count" in result_message.structured_output
+    assert "has_tests" in result_message.structured_output
+    assert isinstance(result_message.structured_output["file_count"], (int, float))
+    assert isinstance(result_message.structured_output["has_tests"], bool)
+
+    # Should find Python files in src/
+    assert result_message.structured_output["file_count"] > 0
+
+
+@pytest.mark.e2e
+@pytest.mark.asyncio
+async def test_nested_structured_output():
+    """Test structured output with nested objects and arrays."""
+
+    # Define a schema with nested structure
+    schema = {
+        "type": "object",
+        "properties": {
+            "analysis": {
+                "type": "object",
+                "properties": {
+                    "word_count": {"type": "number"},
+                    "character_count": {"type": "number"},
+                },
+                "required": ["word_count", "character_count"],
+            },
+            "words": {
+                "type": "array",
+                "items": {"type": "string"},
+            },
+        },
+        "required": ["analysis", "words"],
+    }
+
+    options = ClaudeAgentOptions(
+        output_format={"type": "json_schema", "schema": schema},
+        permission_mode="acceptEdits",
+    )
+
+    result_message = None
+    async for message in query(
+        prompt="Analyze this text: 'Hello world'. Provide word count, character count, and list of words.",
+        options=options,
+    ):
+        if isinstance(message, ResultMessage):
+            result_message = message
+
+    # Verify result
+    assert result_message is not None
+    assert not result_message.is_error
+    assert result_message.structured_output is not None
+
+    # Check nested structure
+    output = result_message.structured_output
+    assert "analysis" in output
+    assert "words" in output
+    assert output["analysis"]["word_count"] == 2
+    assert output["analysis"]["character_count"] == 11  # "Hello world"
+    assert len(output["words"]) == 2
+
+
+@pytest.mark.e2e
+@pytest.mark.asyncio
+async def test_structured_output_with_enum():
+    """Test structured output with enum constraints requiring code analysis."""
+
+    schema = {
+        "type": "object",
+        "properties": {
+            "has_tests": {"type": "boolean"},
+            "test_framework": {
+                "type": "string",
+                "enum": ["pytest", "unittest", "nose", "unknown"],
+            },
+            "test_count": {"type": "number"},
+        },
+        "required": ["has_tests", "test_framework"],
+    }
+
+    options = ClaudeAgentOptions(
+        output_format={"type": "json_schema", "schema": schema},
+        permission_mode="acceptEdits",
+        cwd=".",
+    )
+
+    result_message = None
+    async for message in query(
+        prompt="Search for test files in the tests/ directory. Determine which test framework is being used (pytest/unittest/nose) and count how many test files exist. Use Grep to search for framework imports.",
+        options=options,
+    ):
+        if isinstance(message, ResultMessage):
+            result_message = message
+
+    # Verify result
+    assert result_message is not None
+    assert not result_message.is_error
+    assert result_message.structured_output is not None
+
+    # Check enum values are valid
+    output = result_message.structured_output
+    assert output["test_framework"] in ["pytest", "unittest", "nose", "unknown"]
+    assert isinstance(output["has_tests"], bool)
+
+    # This repo uses pytest
+    assert output["has_tests"] is True
+    assert output["test_framework"] == "pytest"
+
+
+@pytest.mark.e2e
+@pytest.mark.asyncio
+async def test_structured_output_with_tools():
+    """Test structured output when agent uses tools."""
+
+    # Schema for file analysis
+    schema = {
+        "type": "object",
+        "properties": {
+            "file_count": {"type": "number"},
+            "has_readme": {"type": "boolean"},
+        },
+        "required": ["file_count", "has_readme"],
+    }
+
+    options = ClaudeAgentOptions(
+        output_format={"type": "json_schema", "schema": schema},
+        permission_mode="acceptEdits",
+        cwd=tempfile.gettempdir(),  # Cross-platform temp directory
+    )
+
+    result_message = None
+    async for message in query(
+        prompt="Count how many files are in the current directory and check if there's a README file. Use tools as needed.",
+        options=options,
+    ):
+        if isinstance(message, ResultMessage):
+            result_message = message
+
+    # Verify result
+    assert result_message is not None
+    assert not result_message.is_error
+    assert result_message.structured_output is not None
+
+    # Check structure
+    output = result_message.structured_output
+    assert "file_count" in output
+    assert "has_readme" in output
+    assert isinstance(output["file_count"], (int, float))
+    assert isinstance(output["has_readme"], bool)
+    assert output["file_count"] >= 0  # Should be non-negative
diff --git a/src/claude_agent_sdk/_internal/message_parser.py b/src/claude_agent_sdk/_internal/message_parser.py
index 6532a204..694c52c3 100644
--- a/src/claude_agent_sdk/_internal/message_parser.py
+++ b/src/claude_agent_sdk/_internal/message_parser.py
@@ -149,6 +149,7 @@ def parse_message(data: dict[str, Any]) -> Message:
                     total_cost_usd=data.get("total_cost_usd"),
                     usage=data.get("usage"),
                     result=data.get("result"),
+                    structured_output=data.get("structured_output"),
                 )
             except KeyError as e:
                 raise MessageParseError(
diff --git a/src/claude_agent_sdk/_internal/transport/subprocess_cli.py b/src/claude_agent_sdk/_internal/transport/subprocess_cli.py
index d669a412..433c47e6 100644
--- a/src/claude_agent_sdk/_internal/transport/subprocess_cli.py
+++ b/src/claude_agent_sdk/_internal/transport/subprocess_cli.py
@@ -215,7 +215,24 @@ def _build_command(self) -> list[str]:
                 # Flag with value
                 cmd.extend([f"--{flag}", str(value)])
 
+        if self._options.max_thinking_tokens is not None:
+            cmd.extend(
+                ["--max-thinking-tokens", str(self._options.max_thinking_tokens)]
+            )
+
+        # Extract schema from output_format structure if provided
+        # Expected: {"type": "json_schema", "schema": {...}}
+        if (
+            self._options.output_format is not None
+            and isinstance(self._options.output_format, dict)
+            and self._options.output_format.get("type") == "json_schema"
+        ):
+            schema = self._options.output_format.get("schema")
+            if schema is not None:
+                cmd.extend(["--json-schema", json.dumps(schema)])
+
         # Add prompt handling based on mode
+        # IMPORTANT: This must come AFTER all flags because everything after "--" is treated as arguments
         if self._is_streaming:
             # Streaming mode: use --input-format stream-json
             cmd.extend(["--input-format", "stream-json"])
@@ -223,11 +240,6 @@ def _build_command(self) -> list[str]:
             # String mode: use --print with the prompt
             cmd.extend(["--print", "--", str(self._prompt)])
 
-        if self._options.max_thinking_tokens is not None:
-            cmd.extend(
-                ["--max-thinking-tokens", str(self._options.max_thinking_tokens)]
-            )
-
         # Check if command line is too long (Windows limitation)
         cmd_str = " ".join(cmd)
         if len(cmd_str) > _CMD_LENGTH_LIMIT and self._options.agents:
diff --git a/src/claude_agent_sdk/types.py b/src/claude_agent_sdk/types.py
index e375bee2..406c204c 100644
--- a/src/claude_agent_sdk/types.py
+++ b/src/claude_agent_sdk/types.py
@@ -492,6 +492,7 @@ class ResultMessage:
     total_cost_usd: float | None = None
     usage: dict[str, Any] | None = None
     result: str | None = None
+    structured_output: Any = None
 
 
 @dataclass
@@ -558,6 +559,9 @@ class ClaudeAgentOptions:
     plugins: list[SdkPluginConfig] = field(default_factory=list)
     # Max tokens for thinking blocks
     max_thinking_tokens: int | None = None
+    # Output format for structured outputs (matches Messages API structure)
+    # Example: {"type": "json_schema", "schema": {"type": "object", "properties": {...}}}
+    output_format: dict[str, Any] | None = None
 
 
 # SDK Control Protocol