diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
index 9358162c2..8e9c209f0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
@@ -33,6 +33,9 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.util.*;
+import java.io.*;
+
+
 /**
  * Merges intervals based on reads which overlap them.
  */
@@ -111,6 +114,15 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
      * @return a linked list of sorted, merged intervals.
      */
     private LinkedList<GenomeLoc> parseIntervals(List<String> intervalsSource) {
+
+		// ignore zero-length intervals files.
+		for (int i = 0; i < intervalsSource.size(); i++) 
+		{
+			File f = new File(intervalsSource.get(i));
+			long size = f.length();
+			if (size == 0) { intervalsSource.remove(i); }
+		}
+
         List<GenomeLoc> parsedIntervals = GenomeAnalysisEngine.parseIntervalRegion(intervalsSource);
         GenomeLocSortedSet intervalSortedSet = new GenomeLocSortedSet();
         for ( GenomeLoc parsedInterval : parsedIntervals )
@@ -118,4 +130,4 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
 
         return new LinkedList<GenomeLoc>( intervalSortedSet );
     }
-}
\ No newline at end of file
+}