diff --git a/doc/doxygen/Makefile b/doc/doxygen/Makefile
index c9d0c22fed..90188c15c5 100644
--- a/doc/doxygen/Makefile
+++ b/doc/doxygen/Makefile
@@ -1,3 +1,10 @@
+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 |\
+    grep '/include$$' |\
+    sed 's/.*/\"$(subst /,\/,${RIOTBASE})\/\0\"/')
+
 .PHONY: doc
 doc: html
 
diff --git a/doc/doxygen/riot.doxyfile b/doc/doxygen/riot.doxyfile
index 00ae19be94..dec6cd9e69 100644
--- a/doc/doxygen/riot.doxyfile
+++ b/doc/doxygen/riot.doxyfile
@@ -161,7 +161,7 @@ STRIP_FROM_PATH        =
 # specify the list of include paths that are normally passed to the compiler
 # using the -I flag.
 
-STRIP_FROM_INC_PATH    =
+STRIP_FROM_INC_PATH    = $(STRIP_FROM_INC_PATH_LIST) # Exported from Makefile.
 
 # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
 # less readable) file names. This can be useful is your file systems doesn't