diff --git a/Makefile b/Makefile
index 7ea74eaae2..7703cc04eb 100644
--- a/Makefile
+++ b/Makefile
@@ -210,11 +210,11 @@ menuconfig:
 endif
 
 $(NUTTX_SRC):
-	$(Q) if [ -d $(NUTTX_SRC) ]; then ./Tools/check_submodules.sh; else echo ""; echo ""; echo "NuttX submodule missing, doing auto checkout"; git submodule init; git submodule update; fi
+	$(Q) (./Tools/check_submodules.sh)
 
 .PHONY: checksubmodules
 checksubmodules:
-	$(Q) if [ -d $(MAVLINK_SRC) ]; then ./Tools/check_submodules.sh; else echo ""; echo ""; echo "MAVLink submodule missing, doing auto checkout"; git submodule init; git submodule update; fi
+	$(Q) (./Tools/check_submodules.sh)
 
 #
 # Testing targets
diff --git a/Tools/check_submodules.sh b/Tools/check_submodules.sh
index c431e82252..d31c1588c7 100755
--- a/Tools/check_submodules.sh
+++ b/Tools/check_submodules.sh
@@ -1,18 +1,34 @@
 #!/bin/sh
-STATUSRETVAL=$(git status --porcelain | grep -i "M mavlink/include/mavlink/v1.0")
-if [ "$STATUSRETVAL" == "" ]; then
-	echo "checked mavlink submodule, correct version found"
+
+if [ -d NuttX/nuttx ];
+	then
+	STATUSRETVAL=$(git status --porcelain | grep -i "mavlink/include/mavlink/v1.0")
+	if [ "$STATUSRETVAL" == "" ]; then
+		echo "Checked mavlink submodule, correct version found"
+	else
+		echo "mavlink sub repo not at correct version. Try 'git submodule update'"
+		echo "or follow instructions on http://pixhawk.org/dev/git/submodules"
+		exit 1
+	fi
 else
-	echo "mavlink sub repo not at correct version. Try 'git submodule update'"
-	exit 1
+	git submodule init;
+	git submodule update;
 fi
 
-STATUSRETVAL=$(git status --porcelain | grep -i "M NuttX")
-if [ "$STATUSRETVAL" == "" ]; then
-	echo "checked NuttX submodule, correct version found"
+
+if [ -d mavlink/include/mavlink/v1.0 ];
+	then
+	STATUSRETVAL=$(git status --porcelain | grep -i "NuttX")
+	if [ "$STATUSRETVAL" == "" ]; then
+		echo "Checked NuttX submodule, correct version found"
+	else
+		echo "NuttX sub repo not at correct version. Try 'git submodule update'"
+		echo "or follow instructions on http://pixhawk.org/dev/git/submodules"
+		exit 1
+	fi
 else
-	echo "NuttX sub repo not at correct version. Try 'git submodule update'"
-	exit 1
+	git submodule init;
+	git submodule update;
 fi
 
 exit 0