diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
index 7ce40ad98..f66eeed4e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
@@ -147,11 +147,7 @@ public class DiffEngine {
      * @param diffs the list of differences to summarize
      */
     public void reportSummarizedDifferences(List<Difference> diffs, SummaryReportParams params ) {
-        printSummaryReport(summarizeDifferences(diffs), params );
-    }
-
-    public List<Difference> summarizeDifferences(List<Difference> diffs) {
-        return summarizedDifferencesOfPaths(diffs);
+        printSummaryReport(summarizedDifferencesOfPaths(diffs, params.maxRawDiffsToSummarize), params );
     }
 
     final protected static String[] diffNameToPath(String diffName) {
@@ -165,10 +161,11 @@ public class DiffEngine {
             diffs.add(new Difference(diff));
         }
 
-        return summarizedDifferencesOfPaths(diffs);
+        return summarizedDifferencesOfPaths(diffs, -1);
     }
 
-    protected List<Difference> summarizedDifferencesOfPaths(List<? extends Difference> singletonDiffs) {
+    private Map<String, Difference> initialPairwiseSummaries(final List<? extends Difference> singletonDiffs,
+                                                             final int maxRawDiffsToSummarize) {
         Map<String, Difference> summaries = new HashMap<String, Difference>();
 
         // create the initial set of differences
@@ -184,10 +181,20 @@ public class DiffEngine {
                     Difference sumDiff = new Difference(path, diffPath2.getMaster(), diffPath2.getTest());
                     sumDiff.setCount(0);
                     addSummaryIfMissing(summaries, sumDiff);
+
+                    if ( maxRawDiffsToSummarize != -1 && summaries.size() > maxRawDiffsToSummarize)
+                        return summaries;
                 }
             }
         }
 
+        return summaries;
+    }
+
+    protected List<Difference> summarizedDifferencesOfPaths(final List<? extends Difference> singletonDiffs,
+                                                            final int maxRawDiffsToSummarize) {
+        Map<String, Difference> summaries = initialPairwiseSummaries(singletonDiffs, maxRawDiffsToSummarize);
+
         // count differences
         for ( Difference diffPath : singletonDiffs ) {
             for ( Difference sumDiff : summaries.values() ) {
@@ -360,17 +367,23 @@ public class DiffEngine {
     }
 
     public static class SummaryReportParams {
-        PrintStream out = System.out;
-        int maxItemsToDisplay = 0;
-        int maxCountOneItems = 0;
-        int minSumDiffToShow = 0;
+        final PrintStream out;
+        final int maxItemsToDisplay;
+        final int maxCountOneItems;
+        final int minSumDiffToShow;
+        final int maxRawDiffsToSummarize;
         boolean descending = true;
 
-        public SummaryReportParams(PrintStream out, int maxItemsToDisplay, int maxCountOneItems, int minSumDiffToShow) {
+        public SummaryReportParams(PrintStream out,
+                                   int maxItemsToDisplay,
+                                   int maxCountOneItems,
+                                   int minSumDiffToShow,
+                                   int maxRawDiffsToSummarize) {
             this.out = out;
             this.maxItemsToDisplay = maxItemsToDisplay;
             this.maxCountOneItems = maxCountOneItems;
             this.minSumDiffToShow = minSumDiffToShow;
+            this.maxRawDiffsToSummarize = maxRawDiffsToSummarize;
         }
 
         public void setDescending(boolean descending) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
index 04437fdd1..21de6135f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
@@ -162,6 +162,10 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
     @Argument(fullName="maxObjectsToRead", shortName="motr", doc="Max. number of objects to read from the files.  -1 [default] means unlimited", required=false)
     int MAX_OBJECTS_TO_READ = -1;
 
+    @Argument(fullName="maxRawDiffsToSummary", shortName="maxRawDiffsToSummary", doc="Max. number of objects to read from the files.  -1 [default] means unlimited", required=false)
+    int maxRawDiffsToSummary = -1;
+
+
     /**
      * The max number of differences to display when summarizing.  For example, if there are 10M differences, but
      * maxDiffs is 10, then the comparison aborts after first ten summarized differences are shown.  Note that
@@ -232,13 +236,14 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
 //        out.println(test.toString());
 
         List<Difference> diffs = diffEngine.diff(master, test);
+        out.printf("  Done computing diff, n = %d%n", diffs.size());
         if ( showItemizedDifferences ) {
             out.printf("Itemized results%n");
             for ( Difference diff : diffs )
                 out.printf("DIFF: %s%n", diff.toString());
         }
 
-        DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_DIFFS, MAX_COUNT1_DIFFS, minCountForDiff);
+        DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_DIFFS, MAX_COUNT1_DIFFS, minCountForDiff, maxRawDiffsToSummary);
         params.setDescending(false);
         diffEngine.reportSummarizedDifferences(diffs, params);
     }
diff --git a/public/java/test/org/broadinstitute/sting/MD5DB.java b/public/java/test/org/broadinstitute/sting/MD5DB.java
index e756c9864..6b62cb3cd 100644
--- a/public/java/test/org/broadinstitute/sting/MD5DB.java
+++ b/public/java/test/org/broadinstitute/sting/MD5DB.java
@@ -250,7 +250,7 @@ public class MD5DB {
                     // TODO -- capture output and put in log
                     final ByteArrayOutputStream baos = new ByteArrayOutputStream();
                     final PrintStream ps = new PrintStream(baos);
-                    DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(ps, 20, 10, 0);
+                    DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(ps, 20, 10, 0, MAX_RECORDS_TO_READ);
                     boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), MAX_RECORDS_TO_READ, params);
                     if ( success ) {
                         final String content = baos.toString();