diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index c26e1fab46fccb27380437bd6f808bc69cb51f4a..74f295b0fd2e64d528d470bab33ab4e6799268a9 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -2294,6 +2294,10 @@ sub cleanup_sources_file{
   open (DEL, ">>$dir/cleanup.sql") || die "Could not open $dir/cleanup.sql\n";
 
   if ($id =~ m/\w/){
+    print DEL "DELETE unmapped_object ";
+    print DEL    "FROM unmapped_object ";
+    print DEL      "WHERE type = 'xref'\n";
+
     print DEL "DELETE external_synonym ";
     print DEL     "FROM external_synonym, xref ";
     print DEL       "WHERE external_synonym.xref_id = xref.xref_id ";