diff --git modules/system/system.admin.inc modules/system/system.admin.inc
index 0b6e456..edecf72 100644
--- modules/system/system.admin.inc
+++ modules/system/system.admin.inc
@@ -1729,13 +1729,17 @@ function system_clear_page_cache_submit($form, &$form_state) {
  * @see system_settings_form()
  */
 function system_file_system_settings() {
+  $form = array(
+    '#validate' => array('system_file_system_settings_validate'),
+    '#submit' => array('system_file_system_settings_submit'),
+  );
+
   $form['file_public_path'] = array(
     '#type' => 'textfield',
     '#title' => t('Public file system path'),
     '#default_value' => variable_get('file_public_path', conf_path() . '/files'),
     '#maxlength' => 255,
     '#description' => t('A local file system path where public files will be stored. This directory must exist and be writable by Drupal. This directory must be relative to the Drupal installation directory and be accessible over the web.'),
-    '#after_build' => array('system_check_directory'),
   );
 
   $form['file_private_path'] = array(
@@ -1744,7 +1748,6 @@ function system_file_system_settings() {
     '#default_value' => variable_get('file_private_path', ''),
     '#maxlength' => 255,
     '#description' => t('A local file system path where private files will be stored. This directory must exist and be writable by Drupal. This directory should not be accessible over the web.'),
-    '#after_build' => array('system_check_directory'),
   );
 
   $form['file_temporary_path'] = array(
@@ -1753,7 +1756,6 @@ function system_file_system_settings() {
     '#default_value' => variable_get('file_temporary_path', file_directory_temp()),
     '#maxlength' => 255,
     '#description' => t('A local file system path where temporary files will be stored. This directory should not be accessible over the web.'),
-    '#after_build' => array('system_check_directory'),
   );
   // Any visible, writeable wrapper can potentially be used for the files
   // directory, including a remote file system that integrates with a CDN.
@@ -1775,6 +1777,34 @@ function system_file_system_settings() {
 }
 
 /**
+ * Checks that the private and temporary directories do not resolve to the same
+ * directory as the public directory.
+ */
+function system_file_system_settings_validate($form, &$form_state) {
+  $resolved_public_path = realpath($form['file_public_path']['#value']);
+  $resolved_private_path = realpath($form['file_private_path']['#value']);
+  $resolved_temporary_path = realpath($form['file_temporary_path']['#value']);
+
+  if ($resolved_public_path == $resolved_private_path) {
+    form_set_error('file_private_path', t('The private file system path must not be the same as the public file system path.'));
+  }
+
+  if ($resolved_public_path == $resolved_temporary_path) {
+    form_set_error('file_temporary_path', t('The temporary directory must not be the same as the public file system path.'));
+  }
+}
+
+/**
+ * Check to see if the public, private, and temporary paths exist or can be
+ * created if needed.
+ */
+function system_file_system_settings_submit($form, &$form_state) {
+  system_check_directory($form['file_public_path']);
+  system_check_directory($form['file_private_path']);
+  system_check_directory($form['file_temporary_path']);
+}
+
+/**
  * Form builder; Configure site image toolkit usage.
  *
  * @ingroup forms