diff --git a/doc/doxygen/Makefile b/doc/doxygen/Makefile
index 90188c15c..d001fc024 100644
--- a/doc/doxygen/Makefile
+++ b/doc/doxygen/Makefile
@@ -1,7 +1,7 @@
 RIOTBASE=$(shell git rev-parse --show-toplevel)
 # Generate list of quoted absolute include paths. Evaluated in riot.doxyfile.
 export STRIP_FROM_INC_PATH_LIST=$(shell \
-    git ls-tree -dr --full-tree --name-only HEAD |\
+    git ls-tree -dr --full-tree --name-only HEAD core drivers sys |\
     grep '/include$$' |\
     sed 's/.*/\"$(subst /,\/,${RIOTBASE})\/\0\"/')