diff --git a/misc-scripts/id_mapping/utils/id_mapping_clean.sql b/misc-scripts/id_mapping/utils/id_mapping_clean.sql
index 4806b44252bae53cd512d6e40818406114f07c38..60a18581114f5c5d89104d5ea743e895b0ecec89 100644
--- a/misc-scripts/id_mapping/utils/id_mapping_clean.sql
+++ b/misc-scripts/id_mapping/utils/id_mapping_clean.sql
@@ -33,3 +33,13 @@ DELETE FROM stable_id_event;
 DELETE FROM gene_archive;
 DELETE FROM peptide_archive;
 
+# drop backup tables
+DROP TABLE gene_stable_id_bak;
+DROP TABLE transcript_stable_id_bak;
+DROP TABLE translation_stable_id_bak;
+DROP TABLE exon_stable_id_bak;
+DROP TABLE mapping_session_bak;
+DROP TABLE stable_id_event_bak;
+DROP TABLE gene_archive_bak;
+DROP TABLE peptide_archive_bak;
+