diff --git a/lib/db/upgrade.php b/lib/db/upgrade.php
index 0bd812003ff..bf1cb78ce4b 100644
--- a/lib/db/upgrade.php
+++ b/lib/db/upgrade.php
@@ -2172,5 +2172,19 @@ function xmldb_main_upgrade($oldversion) {
         upgrade_main_savepoint(true, 2013051400.06);
     }
 
+    if ($oldversion < 2013051400.09) {
+
+        // Remove orphan repository instances.
+        $sql = 'SELECT contextid FROM {repository_instances} ri
+                WHERE NOT EXISTS (
+                    SELECT id FROM {context} c
+                        WHERE c.id = ri.contextid)';
+        $ids = $DB->get_fieldset_sql($sql);
+        $DB->delete_records_list('repository_instances', 'contextid', $ids);
+
+        // Main savepoint reached.
+        upgrade_main_savepoint(true, 2013051400.09);
+    }
+
     return true;
 }
diff --git a/version.php b/version.php
index 394c58e80bd..be062dd964c 100644
--- a/version.php
+++ b/version.php
@@ -29,7 +29,7 @@
 
 defined('MOODLE_INTERNAL') || die();
 
-$version  = 2013051400.08;              // 20130514      = branching date YYYYMMDD - do not modify!
+$version  = 2013051400.09;              // 20130514      = branching date YYYYMMDD - do not modify!
                                         //         RR    = release increments - 00 in DEV branches
                                         //           .XX = incremental changes