diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index c1b03d002..4707a5060 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -327,9 +327,14 @@ public class GenomeAnalysisEngine {
 			rg_sets.add(groups);
 			
 			for ( SAMReadGroupRecord g : r.getFileHeader().getReadGroups() ) {
-				// use HeaderMerger to translate original read group id from the reader into the read group id in the 
-				// merged stream, and save that remapped read group id to associate it with specific reader
-				groups.add( hm.getReadGroupId(r, g.getReadGroupId()) );
+				if (hm.hasGroupIdDuplicates()) { // Check if there were read group clashes with hasGroupIdDuplicates and if so:
+					// use HeaderMerger to translate original read group id from the reader into the read group id in the
+					// merged stream, and save that remapped read group id to associate it with specific reader
+					groups.add( hm.getReadGroupId(r, g.getReadGroupId()) );
+				}else{
+					// otherwise, pass through the unmapped read groups since this is what Picard does as well
+					groups.add( g.getReadGroupId() );
+				}
 			}
 		}