diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
index 112eb278e..cbd3bc950 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
@@ -246,6 +246,14 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
      */
     private void addNewOverlappingIntervals(GenomeLoc refLocus) {
         GenomeLoc interval = intervalListIterator.peek();
+
+        // skip any intervals with no coverage that we have passed
+        while (interval != null && interval.isBefore(refLocus)) {
+            intervalListIterator.next();                                                                                // discard the interval (we've already added it to the map)
+            interval = intervalListIterator.peek();
+        }
+
+        // add any intervals that overlap this one
         while (interval != null && !interval.isPast(refLocus)) {
             intervalMap.put(interval, createIntervalStatistic(interval));
             intervalListIterator.next();                                                                                // discard the interval (we've already added it to the map)