diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index c86b91b79..6b101ca74 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -381,7 +381,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
             }
         }
 
-        attributes.put(VariantContext.ID_KEY, id);
+        if ( ! id.equals(VCFConstants.EMPTY_ID_FIELD) )
+            attributes.put(VariantContext.ID_KEY, id);
         return attributes;
     }