diff --git a/Doxyfile b/Doxyfile.in
similarity index 99%
rename from Doxyfile
rename to Doxyfile.in
index 7762386ef03e39a5a0f8b653273bb1fefcc52fa3..0b204a096b7304e819331d057989647355c1032a 100644
--- a/Doxyfile
+++ b/Doxyfile.in
@@ -564,12 +564,12 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = doc/manual \
-                         TODO \
-                         BUGS \
-                         PATCHES \
-                         src \
-                         config.h
+INPUT                  = @srcdir@/doc/manual \
+                         @srcdir@/TODO \
+                         @srcdir@/BUGS \
+                         @srcdir@/PATCHES \
+                         @srcdir@/src \
+                         @srcdir@/config.h
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
diff --git a/Makefile.am b/Makefile.am
index cb5277b76802d96bff310129160c1fd014929d59..10735f3458f77a57a9f44fe03ee36ded1fbd6554 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -11,15 +11,23 @@ nobase_dist_pkgdata_DATA = \
 
 SUBDIRS = src doc
 
-EXTRA_DIST = Doxyfile
+EXTRA_DIST = \
+	Doxyfile.in \
+	tools/logger.pl
 
 docs: pdf html doxygen
 
+Doxyfile: $(srcdir)/Doxyfile.in
+	sed -e 's,@srcdir\@,$(srcdir),' $< > $@
+
 doxygen::
-	(cd $(srcdir) && doxygen Doxyfile 2>&1 | perl tools/logger.pl ) > doxygen.log
+	$(MAKE) Doxyfile
+	doxygen Doxyfile 2>&1 | perl $(srcdir)/tools/logger.pl > doxygen.log
+
+distclean-local:
+	rm -rf Doxyfile doxygen
 
-doxygen-clean:
-	rm -f -r doxygen doxygen.log
+DISTCLEANFILES = doxygen.log
 
 MAINTAINERCLEANFILES = \
 	configure \