diff --git a/Doxyfile.in b/Doxyfile.in
index 519bb2f82..f6e3ced0d 100644
--- a/Doxyfile.in
+++ b/Doxyfile.in
@@ -569,7 +569,7 @@ INPUT                  = @srcdir@/doc/manual \
                          @srcdir@/BUGS \
                          @srcdir@/PATCHES.txt \
                          @srcdir@/src \
-                         @srcdir@/config.h
+                         @builddir@/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 fab470466..7d42fd3f7 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -26,6 +26,7 @@ Doxyfile: $(srcdir)/Doxyfile.in
 	  echo "### @@@ -= DO NOT EDIT THIS FILE =- @@@ ###" && \
 	  echo "### @@@ Make changes to Doxyfile.in @@@ ###" && \
 	  sed -e 's,@srcdir\@,$(srcdir),' \
+	    -e 's,@builddir\@,$(builddir),' \
 	    -e 's,@doxygen_as_html\@,$(doxygen_as_html),' \
 	    -e 's,@doxygen_as_pdf\@,$(doxygen_as_pdf),' $< \
 	) > $@