diff --git a/src/mcp/server/lowlevel/server.py b/src/mcp/server/lowlevel/server.py
index ab6a3d15c..638898083 100644
--- a/src/mcp/server/lowlevel/server.py
+++ b/src/mcp/server/lowlevel/server.py
@@ -603,13 +603,16 @@ async def _handle_message(
         raise_exceptions: bool = False,
     ):
         with warnings.catch_warnings(record=True) as w:
-            # TODO(Marcelo): We should be checking if message is Exception here.
-            match message:  # type: ignore[reportMatchNotExhaustive]
+            match message:
                 case RequestResponder(request=types.ClientRequest(root=req)) as responder:
                     with responder:
                         await self._handle_request(message, req, session, lifespan_context, raise_exceptions)
                 case types.ClientNotification(root=notify):
                     await self._handle_notification(notify)
+                case Exception() as error:
+                    logger.exception("Error in message processing: %s", error)
+                    if raise_exceptions:
+                        raise error
 
             for warning in w:
                 logger.info("Warning: %s: %s", warning.category.__name__, warning.message)
diff --git a/tests/server/test_exception_handling.py b/tests/server/test_exception_handling.py
new file mode 100644
index 000000000..6526bb897
--- /dev/null
+++ b/tests/server/test_exception_handling.py
@@ -0,0 +1,121 @@
+"""Test exception handling in lowlevel server message processing."""
+
+import logging
+from unittest.mock import Mock
+
+import anyio
+import pytest
+
+from mcp.server import Server
+from mcp.server.lowlevel import NotificationOptions
+from mcp.server.models import InitializationOptions
+from mcp.server.session import ServerSession
+from mcp.shared.message import SessionMessage
+from mcp.types import ServerCapabilities
+
+
+@pytest.mark.anyio
+async def test_handle_message_with_exception_logging(caplog):
+    """Test that Exception instances passed to _handle_message are properly logged."""
+    server = Server("test")
+    
+    # Create in-memory streams for testing
+    server_to_client_send, server_to_client_receive = anyio.create_memory_object_stream[SessionMessage](10)
+    client_to_server_send, client_to_server_receive = anyio.create_memory_object_stream[SessionMessage](10)
+    
+    # Create a server session
+    session = ServerSession(
+        read_stream=client_to_server_receive,
+        write_stream=server_to_client_send,
+        init_options=InitializationOptions(
+            server_name="test",
+            server_version="1.0.0",
+            capabilities=ServerCapabilities(),
+        ),
+    )
+    
+    # Create a test exception
+    test_exception = ValueError("Test exception for logging")
+    
+    # Test the _handle_message method directly with an Exception
+    with caplog.at_level(logging.ERROR):
+        await server._handle_message(
+            message=test_exception,
+            session=session,
+            lifespan_context=None,
+            raise_exceptions=False,
+        )
+    
+    # Verify that the exception was logged
+    assert len(caplog.records) == 1
+    record = caplog.records[0]
+    assert record.levelno == logging.ERROR
+    assert "Error in message processing" in record.getMessage()
+    assert "Test exception for logging" in record.getMessage()
+
+
+@pytest.mark.anyio
+async def test_handle_message_with_exception_raising():
+    """Test that Exception instances are re-raised when raise_exceptions=True."""
+    server = Server("test")
+    
+    # Create in-memory streams for testing
+    server_to_client_send, server_to_client_receive = anyio.create_memory_object_stream[SessionMessage](10)
+    client_to_server_send, client_to_server_receive = anyio.create_memory_object_stream[SessionMessage](10)
+    
+    # Create a server session
+    session = ServerSession(
+        read_stream=client_to_server_receive,
+        write_stream=server_to_client_send,
+        init_options=InitializationOptions(
+            server_name="test",
+            server_version="1.0.0",
+            capabilities=ServerCapabilities(),
+        ),
+    )
+    
+    # Create a test exception
+    test_exception = ValueError("Test exception for raising")
+    
+    # Test that the exception is re-raised when raise_exceptions=True
+    with pytest.raises(ValueError, match="Test exception for raising"):
+        await server._handle_message(
+            message=test_exception,
+            session=session,
+            lifespan_context=None,
+            raise_exceptions=True,
+        )
+
+
+@pytest.mark.anyio
+async def test_handle_message_with_exception_no_raise():
+    """Test that Exception instances are not re-raised when raise_exceptions=False."""
+    server = Server("test")
+    
+    # Create in-memory streams for testing
+    server_to_client_send, server_to_client_receive = anyio.create_memory_object_stream[SessionMessage](10)
+    client_to_server_send, client_to_server_receive = anyio.create_memory_object_stream[SessionMessage](10)
+    
+    # Create a server session
+    session = ServerSession(
+        read_stream=client_to_server_receive,
+        write_stream=server_to_client_send,
+        init_options=InitializationOptions(
+            server_name="test",
+            server_version="1.0.0",
+            capabilities=ServerCapabilities(),
+        ),
+    )
+    
+    # Create a test exception
+    test_exception = RuntimeError("Test exception for no raising")
+    
+    # Test that the exception is not re-raised when raise_exceptions=False
+    # This should not raise an exception
+    await server._handle_message(
+        message=test_exception,
+        session=session,
+        lifespan_context=None,
+        raise_exceptions=False,
+    )
+    # If we reach this point, the test passed 
\ No newline at end of file