diff --git a/src/calibre/db/backend.py b/src/calibre/db/backend.py
index dee198bfb0..f5ee4fad40 100644
--- a/src/calibre/db/backend.py
+++ b/src/calibre/db/backend.py
@@ -1462,8 +1462,11 @@ class DB:
                 finally:
                     self.reopen()
 
-    def vacuum(self, include_fts_db, include_notes_db):
+    def vacuum(self, include_fts_db, include_notes_db, rebuild_annotations_fts):
         self.execute('VACUUM')
+        if rebuild_annotations_fts:
+            self.execute('INSERT INTO annotations_fts(annotations_fts) VALUES("rebuild");')
+            self.execute('INSERT INTO annotations_fts_stemmed(annotations_fts_stemmed) VALUES("rebuild");')
         if self.fts_enabled and include_fts_db:
             self.fts.vacuum()
         if include_notes_db:
diff --git a/src/calibre/db/cache.py b/src/calibre/db/cache.py
index ad7aa79fc8..146192c008 100644
--- a/src/calibre/db/cache.py
+++ b/src/calibre/db/cache.py
@@ -2999,10 +2999,10 @@ class Cache:
         return self.backend.dump_and_restore(callback=callback, sql=sql)
 
     @write_api
-    def vacuum(self, include_fts_db=False, include_notes_db=True):
+    def vacuum(self, include_fts_db=False, include_notes_db=True, rebuild_annotations_fts=False):
         self.is_doing_rebuild_or_vacuum = True
         try:
-            self.backend.vacuum(include_fts_db, include_notes_db)
+            self.backend.vacuum(include_fts_db, include_notes_db, rebuild_annotations_fts)
         finally:
             self.is_doing_rebuild_or_vacuum = False
 
diff --git a/src/calibre/gui2/dialogs/check_library.py b/src/calibre/gui2/dialogs/check_library.py
index e7b3281278..a96dc3a0a0 100644
--- a/src/calibre/gui2/dialogs/check_library.py
+++ b/src/calibre/gui2/dialogs/check_library.py
@@ -64,6 +64,13 @@ class DBCheck(QDialog):  # {{{
         la.setWordWrap(True)
         l.addWidget(la)
 
+        self.annots = a = QCheckBox(_('Also rebuild the annotations search index'))
+        l.addWidget(a)
+        la = QLabel('<p style="margin-left: 20px; font-style: italic">' + _(
+            'This can be a slow operation, depending on the number of annotations you have.'))
+        la.setWordWrap(True)
+        l.addWidget(la)
+
         self.fts = f = QCheckBox(_('Also compact the Full text search database'))
         l.addWidget(f)
         la = QLabel('<p style="margin-left: 20px; font-style: italic">' + _(
@@ -106,12 +113,13 @@ class DBCheck(QDialog):  # {{{
         QApplication.setOverrideCursor(QCursor(Qt.CursorShape.WaitCursor))
         self.vacuum_started = True
         db = self.db()
-        t = self.thread = Thread(target=self.vacuum, args=(db, self.fts.isChecked(), self.notes.isChecked()), daemon=True, name='VacuumDB')
+        t = self.thread = Thread(target=self.vacuum, args=(
+            db, self.fts.isChecked(), self.notes.isChecked(), self.annots.isChecked()), daemon=True, name='VacuumDB')
         t.start()
 
-    def vacuum(self, db, include_fts_db, include_notes_db):
+    def vacuum(self, db, include_fts_db, include_notes_db, rebuild_annotations_fts):
         try:
-            db.vacuum(include_fts_db, include_notes_db)
+            db.vacuum(include_fts_db, include_notes_db, rebuild_annotations_fts)
         except Exception as e:
             import traceback
             self.error = (as_unicode(e), traceback.format_exc())