diff --git a/doc/mainpage.txt b/doc/mainpage.txt
deleted file mode 100644
index 3a62b4d61..000000000
--- a/doc/mainpage.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-/**
-
-\mainpage The \os Operating System
-
-This is the code documentation for \os. More documentation, including
-feature description, tutorials etc, can be found at
-https://github.com/sics-iot/contiki/wiki.
-
-*/
diff --git a/tests/00-doxygen/Makefile b/tests/00-doxygen/Makefile
index b8d933aee..ba3600b79 100644
--- a/tests/00-doxygen/Makefile
+++ b/tests/00-doxygen/Makefile
@@ -25,7 +25,7 @@
 # OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
 # SUCH DAMAGE.
 
-DOCDIR=../../doc
+DOCDIR=../../tools/doxygen
 
 all: summary
 
diff --git a/doc/Doxyfile b/tools/doxygen/Doxyfile
similarity index 99%
rename from doc/Doxyfile
rename to tools/doxygen/Doxyfile
index 236b3884b..8073a8239 100644
--- a/doc/Doxyfile
+++ b/tools/doxygen/Doxyfile
@@ -827,7 +827,7 @@ EXCLUDE_SYMBOLS        =
 # command).
 
 EXAMPLE_PATH           = . \
-                         ../examples/hello-world
+                         ../../examples/hello-world
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
diff --git a/doc/Makefile b/tools/doxygen/Makefile
similarity index 63%
rename from doc/Makefile
rename to tools/doxygen/Makefile
index c4af84ca1..e370fca6e 100644
--- a/doc/Makefile
+++ b/tools/doxygen/Makefile
@@ -1,16 +1,13 @@
+contiking := ../..
 basedirs	:= os arch
-manuals		:= $(shell find ./ -name "*.txt")
-filetypes	:= -iwholename "*/doc/*.txt"
 empty		:=
 space		:= $(empty) $(empty)
-pwd			:= $(shell cd ..; pwd)
+pwd			:= $(shell cd $(contiking); pwd)
 
 # Doxyfile configuration variables
 export docdir	:= .
-export docdirs
-export docsrc
 export doclatex	:= NO
-export docroot	:= ../
+export docroot	:= $(contiking)
 
 # Get appropriate root for doxygen path cutoff
 ifeq ($(HOST_OS),Windows)
@@ -21,12 +18,12 @@ ifeq ($(HOST_OS),Windows)
   endif
 endif
 
-docdirs = $(sort $(foreach dir,$(basedirs),${shell find ../${dir} -type d -not -path "*/.*" -not -path "*/obj_*"}))
-docsrc = $(docdirs) $(foreach dir,$(docdirs),${shell find $(dir) -type f $(filetypes)}) $(manuals)
+export docdirs = $(sort $(foreach dir,$(basedirs),${shell find $(contiking)/${dir} -type d}))
+export docsrc = $(docdirs) $(foreach dir,$(docdirs) .,${shell find $(dir) -type f -name "*.txt"})
 
 .PHONY: clean html
 
-html:
+html: clean
 	@doxygen Doxyfile
 
 clean:
diff --git a/doc/doc-style.css b/tools/doxygen/doc-style.css
similarity index 100%
rename from doc/doc-style.css
rename to tools/doxygen/doc-style.css
diff --git a/tools/doxygen/mainpage.txt b/tools/doxygen/mainpage.txt
new file mode 100644
index 000000000..49f8de249
--- /dev/null
+++ b/tools/doxygen/mainpage.txt
@@ -0,0 +1,9 @@
+/**
+
+\mainpage \os: The Next Generation Contiki
+
+This page provides API description.
+
+Full documentation can be found on the wiki: https://github.com/contiki-ng/contiki-ng/wiki
+
+*/
diff --git a/doc/modules.txt b/tools/doxygen/modules.txt
similarity index 100%
rename from doc/modules.txt
rename to tools/doxygen/modules.txt
diff --git a/doc/pt-doc.txt b/tools/doxygen/pt-doc.txt
similarity index 100%
rename from doc/pt-doc.txt
rename to tools/doxygen/pt-doc.txt