diff -r 9f2467e13c98 Doc/whatsnew/3.6.rst
--- a/Doc/whatsnew/3.6.rst	Wed Sep 07 16:11:08 2016 -0700
+++ b/Doc/whatsnew/3.6.rst	Wed Sep 07 16:22:33 2016 -0700
@@ -843,6 +843,16 @@
 Deprecated
 ==========
 
+Deprecated Build Options
+------------------------
+
+The ``--with-system-ffi`` configure flag now on by default on non-OSX POSIX
+platforms.  It may be disabled by using ``--without-system-ffi``, but using the
+flag is deprecated and will not be accepted in Python 3.7.  OSX is unaffected
+by this change.  Note that many OS distributors already use the
+``--with-system-ffi`` flag when building their system Python.
+
+
 New Keywords
 ------------
 
diff -r 9f2467e13c98 configure
--- a/configure	Wed Sep 07 16:11:08 2016 -0700
+++ b/configure	Wed Sep 07 16:22:33 2016 -0700
@@ -9842,10 +9842,26 @@
 # Check whether --with-system_ffi was given.
 if test "${with_system_ffi+set}" = set; then :
   withval=$with_system_ffi;
-else
-  with_system_ffi="no"
-fi
-
+fi
+
+
+case "$with_system_ffi" in
+    "")
+        case $ac_sys_system in
+            Darwin)
+                with_system_ffi="no"
+                ;;
+            *)
+                with_system_ffi="yes"
+                ;;
+        esac
+        ;;
+    yes|no)
+        ;;
+    *)
+        as_fn_error $? "--with-system-ffi accepts no arguments" "$LINENO" 5
+        ;;
+esac
 
 if test "$with_system_ffi" = "yes" && test -n "$PKG_CONFIG"; then
     LIBFFI_INCLUDEDIR="`"$PKG_CONFIG" libffi --cflags-only-I 2>/dev/null | sed -e 's/^-I//;s/ *$//'`"
diff -r 9f2467e13c98 configure.ac
--- a/configure.ac	Wed Sep 07 16:11:08 2016 -0700
+++ b/configure.ac	Wed Sep 07 16:22:33 2016 -0700
@@ -2733,9 +2733,25 @@
 # Check for use of the system libffi library
 AC_MSG_CHECKING(for --with-system-ffi)
 AC_ARG_WITH(system_ffi,
-            AS_HELP_STRING([--with-system-ffi], [build _ctypes module using an installed ffi library]),
-            [],
-            [with_system_ffi="no"])
+            AS_HELP_STRING([--with-system-ffi], [build _ctypes module using an installed ffi library]),,,)
+
+case "$with_system_ffi" in
+    "")
+        case $ac_sys_system in
+            Darwin)
+                with_system_ffi="no"
+                ;;
+            *)
+                with_system_ffi="yes"
+                ;;
+        esac
+        ;;
+    yes|no)
+        ;;
+    *)
+        AC_MSG_ERROR([--with-system-ffi accepts no arguments])
+        ;;
+esac
 
 if test "$with_system_ffi" = "yes" && test -n "$PKG_CONFIG"; then
     LIBFFI_INCLUDEDIR="`"$PKG_CONFIG" libffi --cflags-only-I 2>/dev/null | sed -e 's/^-I//;s/ *$//'`"
diff -r 9f2467e13c98 setup.py
--- a/setup.py	Wed Sep 07 16:11:08 2016 -0700
+++ b/setup.py	Wed Sep 07 16:22:33 2016 -0700
@@ -1911,6 +1911,9 @@
             if host_platform == 'darwin':
                 return self.configure_ctypes_darwin(ext)
 
+            print('warning: building with the bundled copy of libffi is'
+                  ' deprecated on this platform.  It will not be'
+                  ' distributed with Python 3.7')
             srcdir = sysconfig.get_config_var('srcdir')
             ffi_builddir = os.path.join(self.build_temp, 'libffi')
             ffi_srcdir = os.path.abspath(os.path.join(srcdir, 'Modules',
@@ -2007,13 +2010,14 @@
                      libraries=math_libs)
         self.extensions.extend([ext, ext_test])
 
-        if not '--with-system-ffi' in sysconfig.get_config_var("CONFIG_ARGS"):
-            return
-
         if host_platform == 'darwin':
+            if '--with-system-ffi' not in sysconfig.get_config_var("CONFIG_ARGS"):
+                return
             # OS X 10.5 comes with libffi.dylib; the include files are
             # in /usr/include/ffi
             inc_dirs.append('/usr/include/ffi')
+        elif '--without-system-ffi' in sysconfig.get_config_var("CONFIG_ARGS"):
+            return
 
         ffi_inc = [sysconfig.get_config_var("LIBFFI_INCLUDEDIR")]
         if not ffi_inc or ffi_inc[0] == '':