diff --git a/tools/cooja/config/external_tools_linux.config b/tools/cooja/config/external_tools_linux.config
index 1c9ee9cb1..4c3687cc2 100644
--- a/tools/cooja/config/external_tools_linux.config
+++ b/tools/cooja/config/external_tools_linux.config
@@ -22,7 +22,7 @@ CONTIKI_STANDARD_PROCESSES = sensors_process;etimer_process
 CONTIKI_MAIN_TEMPLATE_FILENAME = contiki_template.c
 CORECOMM_TEMPLATE_FILENAME = corecomm_template.java
 PATH_JAVAC = javac
-DEFAULT_PROJECTDIRS = ../apps/mrm;../apps/mspsim
+DEFAULT_PROJECTDIRS = ../apps/mrm;../apps/mspsim;../apps/avrora
 
 PARSE_WITH_COMMAND=false
 PARSE_COMMAND=nm -a $(LIBFILE)
diff --git a/tools/cooja/config/external_tools_linux_64.config b/tools/cooja/config/external_tools_linux_64.config
index 943579ba4..cc671103b 100644
--- a/tools/cooja/config/external_tools_linux_64.config
+++ b/tools/cooja/config/external_tools_linux_64.config
@@ -22,7 +22,7 @@ CONTIKI_STANDARD_PROCESSES = sensors_process;etimer_process
 CONTIKI_MAIN_TEMPLATE_FILENAME = contiki_template.c
 CORECOMM_TEMPLATE_FILENAME = corecomm_template.java
 PATH_JAVAC = javac
-DEFAULT_PROJECTDIRS = ../apps/mrm;../apps/mspsim
+DEFAULT_PROJECTDIRS = ../apps/mrm;../apps/mspsim;../apps/avrora
 
 PARSE_WITH_COMMAND=false
 PARSE_COMMAND=nm -a $(LIBFILE)
diff --git a/tools/cooja/config/external_tools_macosx.config b/tools/cooja/config/external_tools_macosx.config
index b1df1858f..2f7997482 100644
--- a/tools/cooja/config/external_tools_macosx.config
+++ b/tools/cooja/config/external_tools_macosx.config
@@ -22,7 +22,7 @@ CONTIKI_STANDARD_PROCESSES = sensors_process;etimer_process
 CONTIKI_MAIN_TEMPLATE_FILENAME = contiki_template.c
 CORECOMM_TEMPLATE_FILENAME = corecomm_template.java
 PATH_JAVAC = javac
-DEFAULT_PROJECTDIRS = ../apps/mrm;../apps/mspsim
+DEFAULT_PROJECTDIRS = ../apps/mrm;../apps/mspsim;../apps/avrora
 
 PARSE_WITH_COMMAND = true
 PARSE_COMMAND = nmandsize $(LIBFILE)