diff --git a/mayan/apps/document_indexing/api.py b/mayan/apps/document_indexing/api.py
index a0c0c46004..b282c43b12 100644
--- a/mayan/apps/document_indexing/api.py
+++ b/mayan/apps/document_indexing/api.py
@@ -76,11 +76,10 @@ def delete_empty_index_nodes():
     Delete empty index instance nodes
     """
 
-    for instance_node in IndexInstanceNode.objects.filter(documents__isnull=True):
+    for instance_node in IndexInstanceNode.objects.filter(documents__isnull=True, parent__isnull=False):
         task_delete_empty_index_nodes_recursive(instance_node)
 
 
-
 def task_delete_empty_index_nodes_recursive(instance_node):
     """
     Calls itself recursively deleting empty index instance nodes up to root
diff --git a/mayan/apps/document_indexing/tests.py b/mayan/apps/document_indexing/tests.py
index 32ffb5f928..9925e71b8a 100644
--- a/mayan/apps/document_indexing/tests.py
+++ b/mayan/apps/document_indexing/tests.py
@@ -65,12 +65,12 @@ class IndexTestCase(TestCase):
 
         # Check node instance is destoyed when no metadata is available
         self.document.metadata.get(metadata_type=metadata_type).delete()
-        self.failUnlessEqual(list(IndexInstanceNode.objects.values_list('value', flat=True)), [])
+        self.failUnlessEqual(list(IndexInstanceNode.objects.values_list('value', flat=True)), [u''])
 
         # Add document metadata value again to trigger index node instance creation
         self.document.metadata.create(metadata_type=metadata_type, value='0003')
         self.failUnlessEqual(list(IndexInstanceNode.objects.values_list('value', flat=True)), [u'', u'0003'])
 
-        # Check node instance is destoyed when no documents are contained
+        # Check node instance is destroyed when no documents are contained
         self.document.delete()
-        self.failUnlessEqual(list(IndexInstanceNode.objects.values_list('value', flat=True)), [])
+        self.failUnlessEqual(list(IndexInstanceNode.objects.values_list('value', flat=True)), [u''])