--- a/configure.ac
+++ b/configure.ac
@@ -2857,6 +2857,7 @@
 AC_CONFIG_FILES([
   Makefile 
   doc/Makefile
+  doc/doxyhtml/Makefile
   doc/icons/Makefile
   doc/interpreter/Makefile
   doc/liboctave/Makefile

--- a/doc/Makefile.am
+++ b/doc/Makefile.am
@@ -29,5 +29,5 @@
   texinfo.tex \
   texmf.cnf
 
-SUBDIRS = icons interpreter liboctave refcard
+SUBDIRS = doxyhtml icons interpreter liboctave refcard
 

rename from Doxyfile
rename to doc/doxyhtml/Doxygen.cfg

new file mode 100644
--- /dev/null
+++ b/doc/doxyhtml/Makefile.am
@@ -0,0 +1,32 @@
+# Makefile for Octave's doc/doxyhtml directory
+#
+# Copyright (C) 1993-2012 John W. Eaton
+#
+# This file is part of Octave.
+# 
+# Octave is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation; either version 3 of the License, or (at
+# your option) any later version.
+# 
+# Octave is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+# for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with Octave; see the file COPYING.  If not, see
+# <http://www.gnu.org/licenses/>.
+
+include $(top_srcdir)/build-aux/common.mk
+
+doxyhtml:
+	cd ../..; doxygen doc/doxyhtml/Doxygen.cfg 
+
+EXTRA_DIST = \
+  Doxygen.cfg \
+  Makefile.am \
+  README
+
+maintainer-clean-local:
+	rm -rf `ls | $(GREP) -v Doxygen.cfg | $(GREP) -v Makefile.am | $(GREP) -v Makefile.in | $(GREP) -v README`

new file mode 100644
--- /dev/null
+++ b/doc/doxyhtml/README
@@ -0,0 +1,11 @@
+This directory contains documentation in Doxygen format for
+Octave's source code.  It is not created by default.
+
+To produce Doxygen documentation use
+
+make doxyhtml
+
+Doxygen documentation can be helpful for developers of Octave, but is not
+needed by users of Octave.  In addition, the documentation requires
+approximately 1.2GB of storage space.  For these reasons it is not maintained
+under version control nor distributed in tarballs.