diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
index d16502b1d..896d6e3a2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
@@ -280,7 +280,9 @@ public class LocusIteratorByState extends LocusIterator {
         this.samples = new ArrayList<String>(samples);
         this.readStates = new ReadStateManager(samIterator,readInformation.getDownsamplingMethod());
 
-        if ( this.samples.isEmpty() )
+        // currently the GATK expects this LocusIteratorByState to accept empty sample lists, when
+        // there's no read data.  So we need to throw this error only when samIterator.hasNext() is true
+        if ( this.samples.isEmpty() && samIterator.hasNext() )
             throw new IllegalArgumentException("samples list must not be empty");
     }