diff --git a/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
index a9c3f289d..aeff9a789 100644
--- a/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
@@ -268,8 +268,16 @@ public class AlignmentUtils {
      */
     public static boolean isReadUnmapped(final SAMRecord r) {
         if ( r.getReadUnmappedFlag() ) return true;
-        if ( r.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX ||
-             r.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ) return true;
-        return false;
+
+        // our life would be so much easier if all sam files followed the specs. In reality,
+        // sam files (including those generated by maq or bwa) miss headers alltogether. When
+        // reading such a SAM file, reference name is set, but since there is no sequence dictionary,
+        // null is always returned for referenceIndex. Let's be paranoid here, and make sure that
+        // we do not call the read "unmapped" when it has only reference name set with ref. index missing
+        // or vice versa.
+        if ( ( r.getReferenceIndex() != null && r.getReferenceIndex() != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX
+                || r.getReferenceName() != null && r.getReferenceName() != SAMRecord.NO_ALIGNMENT_REFERENCE_NAME )
+          &&  r.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START ) return false  ;
+        return true;
     }
 }