diff --git a/sphinx/quickstart.py b/sphinx/quickstart.py
index a66f7ecaf..1f0765756 100644
--- a/sphinx/quickstart.py
+++ b/sphinx/quickstart.py
@@ -32,6 +32,9 @@ QUICKSTART_CONF = '''\
 # The contents of this file are pickled, so don't put values in the namespace
 # that aren't pickleable (module imports are okay, they're removed automatically).
 #
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
 # All configuration values have a default; values that are commented out
 # serve to show the default.