diff --git a/Makefile b/Makefile
index 0a85622512..7ea74eaae2 100644
--- a/Makefile
+++ b/Makefile
@@ -104,7 +104,7 @@ DESIRED_FIRMWARES 	 = $(foreach config,$(CONFIGS),$(IMAGE_DIR)$(config).px4)
 STAGED_FIRMWARES	 = $(foreach config,$(KNOWN_CONFIGS),$(IMAGE_DIR)$(config).px4)
 FIRMWARES		 = $(foreach config,$(KNOWN_CONFIGS),$(BUILD_DIR)$(config).build/firmware.px4)
 
-all:			$(DESIRED_FIRMWARES)
+all:			checksubmodules $(DESIRED_FIRMWARES)
 
 #
 # Copy FIRMWARES into the image directory.
@@ -210,9 +210,11 @@ menuconfig:
 endif
 
 $(NUTTX_SRC):
-	@$(ECHO) ""
-	@$(ECHO) "NuttX sources missing - clone https://github.com/PX4/NuttX.git and try again."
-	@$(ECHO) ""
+	$(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
+
+.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
 
 #
 # Testing targets
diff --git a/Tools/check_submodules.sh b/Tools/check_submodules.sh
index 52ea7a1466..c431e82252 100755
--- a/Tools/check_submodules.sh
+++ b/Tools/check_submodules.sh
@@ -7,4 +7,12 @@ else
 	exit 1
 fi
 
+STATUSRETVAL=$(git status --porcelain | grep -i "M NuttX")
+if [ "$STATUSRETVAL" == "" ]; then
+	echo "checked NuttX submodule, correct version found"
+else
+	echo "NuttX sub repo not at correct version. Try 'git submodule update'"
+	exit 1
+fi
+
 exit 0