diff --git a/Makefile b/Makefile
index cd81eaaea..c5fc2d9d2 100644
--- a/Makefile
+++ b/Makefile
@@ -50,6 +50,7 @@ update_doxygen_online:
 	git checkout gh-pages
 	rm -fr html
 	mv /tmp/github-html html
+	cd html ; git rm $(git ls-files --deleted)
 	git commit -m "Doxygen update"
 	git checkout master