diff --git a/plane_mcp/tools/__init__.py b/plane_mcp/tools/__init__.py
index 1ea114e..ef26b3b 100644
--- a/plane_mcp/tools/__init__.py
+++ b/plane_mcp/tools/__init__.py
@@ -1,5 +1,10 @@
 """Tools for Plane MCP Server."""
 
+import logging
+import os
+from collections.abc import Callable
+from types import MappingProxyType
+
 from fastmcp import FastMCP
 
 from plane_mcp.tools.cycles import register_cycle_tools
@@ -11,14 +16,68 @@
 from plane_mcp.tools.work_item_properties import register_work_item_property_tools
 from plane_mcp.tools.work_items import register_work_item_tools
 
+# Map of tool group names to their registration functions (immutable)
+_TOOL_GROUPS: dict[str, Callable[[FastMCP], None]] = {
+    "projects": register_project_tools,
+    "work_items": register_work_item_tools,
+    "cycles": register_cycle_tools,
+    "users": register_user_tools,
+    "modules": register_module_tools,
+    "initiatives": register_initiative_tools,
+    "intake": register_intake_tools,
+    "work_item_properties": register_work_item_property_tools,
+}
+TOOL_GROUPS = MappingProxyType(_TOOL_GROUPS)
+
 
 def register_tools(mcp: FastMCP) -> None:
-    """Register all tools with the MCP server."""
-    register_project_tools(mcp)
-    register_work_item_tools(mcp)
-    register_cycle_tools(mcp)
-    register_user_tools(mcp)
-    register_module_tools(mcp)
-    register_initiative_tools(mcp)
-    register_intake_tools(mcp)
-    register_work_item_property_tools(mcp)
+    """Register tools with the MCP server based on PLANE_TOOLS configuration.
+
+    The PLANE_TOOLS environment variable controls which tool groups are registered:
+    - Not set or empty: Register all tools (default)
+    - Comma-separated list: Register only specified groups
+      Example: PLANE_TOOLS=projects,work_items,users
+    - Exclusion mode (prefix with !): Register all except specified groups
+      Example: PLANE_TOOLS=!cycles,!modules,!initiatives
+
+    Available tool groups: projects, work_items, cycles, users, modules,
+    initiatives, intake, work_item_properties
+    """
+    tools_config = os.getenv("PLANE_TOOLS", "").strip()
+
+    if not tools_config:
+        # Default: register all tools
+        enabled_groups = set(TOOL_GROUPS.keys())
+    elif tools_config.startswith("!"):
+        # Exclusion mode: start with all, remove specified groups
+        # Only items prefixed with ! are excluded
+        items = [t.strip() for t in tools_config.split(",")]
+        excluded = {t[1:] for t in items if t.startswith("!")}
+        unprefixed = {t for t in items if t and not t.startswith("!")}
+        if unprefixed:
+            unprefixed_str = ", ".join(sorted(unprefixed))
+            suggested = ", ".join("!" + t for t in sorted(unprefixed))
+            logging.warning(
+                f"Unprefixed items in exclusion mode will be ignored: {unprefixed_str}. "
+                f"Did you mean: {suggested}?"
+            )
+        # Validate excluded group names
+        invalid = excluded - set(TOOL_GROUPS.keys())
+        if invalid:
+            logging.warning(
+                f"Unknown tool groups in PLANE_TOOLS will be ignored: {', '.join(sorted(invalid))}"
+            )
+        enabled_groups = set(TOOL_GROUPS.keys()) - excluded
+    else:
+        # Inclusion mode: only register specified groups
+        enabled_groups = {t.strip() for t in tools_config.split(",")}
+        # Validate included group names
+        invalid = enabled_groups - set(TOOL_GROUPS.keys()) - {""}
+        if invalid:
+            logging.warning(
+                f"Unknown tool groups in PLANE_TOOLS will be ignored: {', '.join(sorted(invalid))}"
+            )
+
+    for name, register_fn in TOOL_GROUPS.items():
+        if name in enabled_groups:
+            register_fn(mcp)