diff --git a/snakemake/rules.py b/snakemake/rules.py
index e9b2671ef..fcd95abe7 100644
--- a/snakemake/rules.py
+++ b/snakemake/rules.py
@@ -434,7 +434,7 @@ def set_output(self, *output, **kwoutput):
 
     def check_output_duplicates(self):
         """Check ``Namedlist`` for duplicate entries and raise a ``WorkflowError``
-        on problems.
+        on problems. Does not raise if the entry is empty.
         """
         seen = dict()
         idx = None
@@ -444,10 +444,10 @@ def check_output_duplicates(self):
                     idx = 0
                 else:
                     idx += 1
-            if value in seen:
+            if value and value in seen:
                 raise WorkflowError(
                     "Duplicate output file pattern in rule {}. First two "
-                    "duplicate for entries {} and {}".format(
+                    "duplicate for entries {} and {}.".format(
                         self.name, seen[value], name or idx
                     )
                 )