diff --git a/src/claude_agent_sdk/_internal/client.py b/src/claude_agent_sdk/_internal/client.py
index 76323323..d6b787f4 100644
--- a/src/claude_agent_sdk/_internal/client.py
+++ b/src/claude_agent_sdk/_internal/client.py
@@ -128,6 +128,7 @@ async def process_query(
             initialize_timeout=initialize_timeout,
             agents=agents_dict,
             exclude_dynamic_sections=exclude_dynamic_sections,
+            skills=configured_options.skills,
         )
 
         try:
diff --git a/src/claude_agent_sdk/_internal/query.py b/src/claude_agent_sdk/_internal/query.py
index 80b6d93c..30ad2257 100644
--- a/src/claude_agent_sdk/_internal/query.py
+++ b/src/claude_agent_sdk/_internal/query.py
@@ -6,7 +6,7 @@
 import os
 from collections.abc import AsyncIterable, AsyncIterator, Awaitable, Callable
 from contextlib import suppress
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, Literal
 
 import anyio
 from mcp.types import (
@@ -77,6 +77,7 @@ def __init__(
         initialize_timeout: float = 60.0,
         agents: dict[str, dict[str, Any]] | None = None,
         exclude_dynamic_sections: bool | None = None,
+        skills: list[str] | Literal["all"] | None = None,
     ):
         """Initialize Query with transport and callbacks.
 
@@ -90,6 +91,8 @@ def __init__(
             agents: Optional agent definitions to send via initialize
             exclude_dynamic_sections: Optional preset-prompt flag to send via
                 initialize (see ``SystemPromptPreset``)
+            skills: Optional skill allowlist to send via initialize so the CLI
+                can filter which skills are loaded into the system prompt
         """
         self._initialize_timeout = initialize_timeout
         self.transport = transport
@@ -99,6 +102,7 @@ def __init__(
         self.sdk_mcp_servers = sdk_mcp_servers or {}
         self._agents = agents
         self._exclude_dynamic_sections = exclude_dynamic_sections
+        self._skills = skills
 
         # Control protocol state
         self.pending_control_responses: dict[str, anyio.Event] = {}
@@ -160,6 +164,10 @@ async def initialize(self) -> dict[str, Any] | None:
             request["agents"] = self._agents
         if self._exclude_dynamic_sections is not None:
             request["excludeDynamicSections"] = self._exclude_dynamic_sections
+        # 'all' and omitted are equivalent at the wire level (no filter), so
+        # only send the field when it's an explicit list.
+        if isinstance(self._skills, list):
+            request["skills"] = self._skills
 
         # Use longer timeout for initialize since MCP servers may take time to start
         response = await self._send_control_request(
diff --git a/src/claude_agent_sdk/_internal/transport/subprocess_cli.py b/src/claude_agent_sdk/_internal/transport/subprocess_cli.py
index 4b47f115..6733cb4f 100644
--- a/src/claude_agent_sdk/_internal/transport/subprocess_cli.py
+++ b/src/claude_agent_sdk/_internal/transport/subprocess_cli.py
@@ -162,6 +162,44 @@ def _build_settings_value(self) -> str | None:
 
         return json.dumps(settings_obj)
 
+    def _apply_skills_defaults(
+        self,
+    ) -> tuple[list[str], list[str] | None]:
+        """Compute effective allowed_tools and setting_sources for skills.
+
+        When ``options.skills`` is ``"all"``, injects the bare ``Skill`` tool;
+        when it is a list, injects ``Skill(name)`` for each entry. In either
+        case ``setting_sources`` defaults to ``["user", "project"]`` when
+        unset so the CLI discovers installed skills without the caller having
+        to wire up both options manually. ``None`` is a no-op.
+
+        Does not mutate the original options object.
+        """
+        allowed_tools: list[str] = list(self._options.allowed_tools)
+        setting_sources: list[str] | None = (
+            list(self._options.setting_sources)
+            if self._options.setting_sources is not None
+            else None
+        )
+
+        skills = self._options.skills
+        if skills is None:
+            return allowed_tools, setting_sources
+
+        if skills == "all":
+            if "Skill" not in allowed_tools:
+                allowed_tools.append("Skill")
+        else:
+            for name in skills:
+                pattern = f"Skill({name})"
+                if pattern not in allowed_tools:
+                    allowed_tools.append(pattern)
+
+        if setting_sources is None:
+            setting_sources = ["user", "project"]
+
+        return allowed_tools, setting_sources
+
     def _build_command(self) -> list[str]:
         """Build CLI command with arguments."""
         if self._cli_path is None:
@@ -193,8 +231,12 @@ def _build_command(self) -> list[str]:
                 # Preset object - 'claude_code' preset maps to 'default'
                 cmd.extend(["--tools", "default"])
 
-        if self._options.allowed_tools:
-            cmd.extend(["--allowedTools", ",".join(self._options.allowed_tools)])
+        effective_allowed_tools, effective_setting_sources = (
+            self._apply_skills_defaults()
+        )
+
+        if effective_allowed_tools:
+            cmd.extend(["--allowedTools", ",".join(effective_allowed_tools)])
 
         if self._options.max_turns:
             cmd.extend(["--max-turns", str(self._options.max_turns)])
@@ -280,8 +322,8 @@ def _build_command(self) -> list[str]:
         # Agents are always sent via initialize request (matching TypeScript SDK)
         # No --agents CLI flag needed
 
-        if self._options.setting_sources:
-            cmd.extend(["--setting-sources", ",".join(self._options.setting_sources)])
+        if effective_setting_sources:
+            cmd.extend(["--setting-sources", ",".join(effective_setting_sources)])
 
         # Add plugin directories
         if self._options.plugins:
diff --git a/src/claude_agent_sdk/client.py b/src/claude_agent_sdk/client.py
index 64f845fb..7d7911ac 100644
--- a/src/claude_agent_sdk/client.py
+++ b/src/claude_agent_sdk/client.py
@@ -186,6 +186,7 @@ async def _empty_stream() -> AsyncIterator[dict[str, Any]]:
             initialize_timeout=initialize_timeout,
             agents=agents_dict,
             exclude_dynamic_sections=exclude_dynamic_sections,
+            skills=self.options.skills,
         )
 
         # Start reading messages and initialize
diff --git a/src/claude_agent_sdk/types.py b/src/claude_agent_sdk/types.py
index a82a8b9b..75bb9902 100644
--- a/src/claude_agent_sdk/types.py
+++ b/src/claude_agent_sdk/types.py
@@ -1222,6 +1222,28 @@ class ClaudeAgentOptions:
     agents: dict[str, AgentDefinition] | None = None
     # Setting sources to load (user, project, local)
     setting_sources: list[SettingSource] | None = None
+    # Skills to enable for the main session. This is the one place to turn
+    # skills on; you do not need to add ``"Skill"`` to ``allowed_tools`` or
+    # set ``setting_sources`` yourself — the SDK does both when this is set.
+    # The value is also sent on the ``initialize`` control request so a
+    # supporting CLI can filter which skills are loaded into the system prompt
+    # (older CLIs ignore the field).
+    #   * ``None`` (default): skills are off.
+    #   * ``"all"``: enable every discovered skill.
+    #   * ``[name, ...]``: enable only the listed skills. Names match the
+    #     SKILL.md ``name`` / directory name, or ``plugin:skill`` for
+    #     plugin-qualified skills.
+    #
+    # .. note::
+    #     This is a **context filter**, not a sandbox. Unlisted skills are
+    #     hidden from the model's skill listing and cannot be invoked via the
+    #     Skill tool, but their files remain on disk — a session with ``Read``
+    #     or ``Bash`` can still access ``.claude/skills/**`` directly. For
+    #     hard isolation, either omit those files from the working directory,
+    #     bundle the desired subset as a local plugin (``plugins=[...]`` with
+    #     ``setting_sources=None``), or add explicit permission deny rules.
+    #     Do not store secrets in skill files.
+    skills: list[str] | Literal["all"] | None = None
     # Sandbox configuration for bash command isolation.
     # Filesystem and network restrictions are derived from permission rules (Read/Edit/WebFetch),
     # not from these sandbox settings.
diff --git a/tests/test_query.py b/tests/test_query.py
index 30e51c09..1fcb4dea 100644
--- a/tests/test_query.py
+++ b/tests/test_query.py
@@ -59,6 +59,22 @@ def test_initialize_omits_exclude_dynamic_sections_when_unset():
     assert "excludeDynamicSections" not in sent
 
 
+def test_initialize_sends_skills_list():
+    """Query.initialize() includes skills only when it is a list."""
+    sent = _capture_initialize_request(skills=["pdf", "docx"])
+    assert sent["skills"] == ["pdf", "docx"]
+
+    sent_empty = _capture_initialize_request(skills=[])
+    assert sent_empty["skills"] == []
+
+
+def test_initialize_omits_skills_for_none_and_all():
+    """'all' and None both omit skills from initialize (no filter at wire level)."""
+    assert "skills" not in _capture_initialize_request()
+    assert "skills" not in _capture_initialize_request(skills=None)
+    assert "skills" not in _capture_initialize_request(skills="all")
+
+
 def _make_mock_transport(messages, control_requests=None):
     """Create a mock transport that yields messages and optionally sends control requests.
 
diff --git a/tests/test_transport.py b/tests/test_transport.py
index b2c40923..f3a846e4 100644
--- a/tests/test_transport.py
+++ b/tests/test_transport.py
@@ -456,6 +456,95 @@ def test_build_command_setting_sources_included_when_provided(self):
         idx = cmd.index("--setting-sources")
         assert cmd[idx + 1] == "user,project"
 
+    def test_build_command_skills_none_leaves_options_untouched(self):
+        """When skills is None (default), neither allowed_tools nor setting_sources change."""
+        transport = SubprocessCLITransport(
+            prompt="test",
+            options=make_options(),
+        )
+        cmd = transport._build_command()
+        assert "--allowedTools" not in cmd
+        assert "--setting-sources" not in cmd
+
+    def test_build_command_skills_all_enables_skill_tool(self):
+        """skills='all' enables the bare Skill tool and defaults setting_sources."""
+        transport = SubprocessCLITransport(
+            prompt="test",
+            options=make_options(skills="all"),
+        )
+        cmd = transport._build_command()
+        assert "--allowedTools" in cmd
+        assert cmd[cmd.index("--allowedTools") + 1] == "Skill"
+        assert "--setting-sources" in cmd
+        assert cmd[cmd.index("--setting-sources") + 1] == "user,project"
+
+    def test_build_command_skills_empty_list_adds_no_skill_entries(self):
+        """skills=[] is a degenerate subset: setting_sources defaults, no Skill entries."""
+        transport = SubprocessCLITransport(
+            prompt="test",
+            options=make_options(skills=[]),
+        )
+        cmd = transport._build_command()
+        assert "--allowedTools" not in cmd
+        assert "--setting-sources" in cmd
+        assert cmd[cmd.index("--setting-sources") + 1] == "user,project"
+
+    def test_build_command_skills_named_list_uses_skill_patterns(self):
+        """Non-empty skills list adds Skill(name) entries and defaults setting_sources."""
+        transport = SubprocessCLITransport(
+            prompt="test",
+            options=make_options(skills=["pdf", "docx"]),
+        )
+        cmd = transport._build_command()
+        assert "--allowedTools" in cmd
+        assert cmd[cmd.index("--allowedTools") + 1] == "Skill(pdf),Skill(docx)"
+        assert "--setting-sources" in cmd
+        assert cmd[cmd.index("--setting-sources") + 1] == "user,project"
+
+    def test_build_command_skills_merges_with_existing_allowed_tools(self):
+        """skills augment (not replace) an existing allowed_tools list."""
+        transport = SubprocessCLITransport(
+            prompt="test",
+            options=make_options(
+                allowed_tools=["Read", "Write"],
+                skills=["pdf"],
+            ),
+        )
+        cmd = transport._build_command()
+        assert cmd[cmd.index("--allowedTools") + 1] == "Read,Write,Skill(pdf)"
+
+    def test_build_command_skills_preserves_user_setting_sources(self):
+        """When setting_sources is explicitly provided, skills should not override it."""
+        transport = SubprocessCLITransport(
+            prompt="test",
+            options=make_options(
+                skills="all",
+                setting_sources=["local"],
+            ),
+        )
+        cmd = transport._build_command()
+        assert cmd[cmd.index("--setting-sources") + 1] == "local"
+
+    def test_build_command_skills_does_not_mutate_options(self):
+        """Applying skills defaults must not mutate the caller's options object."""
+        options = make_options(allowed_tools=["Read"], skills=["pdf"])
+        transport = SubprocessCLITransport(prompt="test", options=options)
+        transport._build_command()
+        assert options.allowed_tools == ["Read"]
+        assert options.setting_sources is None
+
+    def test_build_command_skills_does_not_duplicate_entries(self):
+        """Injecting Skill entries is idempotent when caller already listed them."""
+        transport = SubprocessCLITransport(
+            prompt="test",
+            options=make_options(
+                allowed_tools=["Skill(pdf)"],
+                skills=["pdf"],
+            ),
+        )
+        cmd = transport._build_command()
+        assert cmd[cmd.index("--allowedTools") + 1] == "Skill(pdf)"
+
     def test_build_command_with_extra_args(self):
         """Test building CLI command with extra_args for future flags."""
         transport = SubprocessCLITransport(