diff --git a/Makefile b/Makefile
index a5252f451bfd..7fb1a2c08305 100644
--- a/Makefile
+++ b/Makefile
@@ -118,9 +118,6 @@ saved-output := $(KBUILD_OUTPUT)
 KBUILD_OUTPUT := $(shell cd $(KBUILD_OUTPUT) && /bin/pwd)
 $(if $(KBUILD_OUTPUT),, \
      $(error output directory "$(saved-output)" does not exist))
-# Check that OUTPUT directory is not the same as where we have kernel src
-$(if $(filter-out $(KBUILD_OUTPUT),$(shell /bin/pwd)),, \
-     $(error Output directory (O=...) specifies kernel src dir))
 
 PHONY += $(MAKECMDGOALS) sub-make
 
diff --git a/scripts/mkmakefile b/scripts/mkmakefile
index ee39facee152..9ad1bd793252 100644
--- a/scripts/mkmakefile
+++ b/scripts/mkmakefile
@@ -11,6 +11,12 @@
 
 
 test ! -r $2/Makefile -o -O $2/Makefile || exit 0
+# Only overwrite automatically generated Makefiles
+# (so we do not overwrite kernel Makefile)
+if ! grep -q Automatically $2/Makefile
+then
+	exit 0
+fi
 echo "  GEN     $2/Makefile"
 
 cat << EOF > $2/Makefile