diff --git a/sort_certificate.py b/sort_certificate.py
index 1658a2e..5115007 100755
--- a/sort_certificate.py
+++ b/sort_certificate.py
@@ -227,13 +227,13 @@ def order_x509(x509_objects, root_issuers):
                         str(root_crt.get_subject()))
         # Double check if our self signed root certificate is not also present
         # as an cross signed intermediate:
-        # - It confuses the ordering process
+        # - It might confuse the ordering process
         if next((x for x in x509_objects
                  if x.get_subject() != x.get_issuer()
                  and x.get_subject() == root_crt.get_subject()), None):
-            raise CertificateComponentException('Both present as intermediate '
-                                                'and root certificate: %s' %
-                                                str(root_crt.get_subject()))
+            logging.warning('Both present as intermediate '
+                            'and root certificate: %s' %
+                            str(root_crt.get_subject()))
     else:
         # Get intermediate cert signed by any root from bundle as anchor, and
         # make that our root