diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 3dc47caa2..6970431ff 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -172,17 +172,24 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
         if (minimumN > 1 && (vcs.size() - numFilteredRecords < minimumN))
             return 0;
         
-        VariantContext mergedVC;
+        List<VariantContext> mergedVCs = new ArrayList<VariantContext>();
         if ( master ) {
-             mergedVC = VariantContextUtils.masterMerge(vcs, "master");
+            mergedVCs.add(VariantContextUtils.masterMerge(vcs, "master"));
         } else {
-            mergedVC = VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(),vcs, priority, filteredRecordsMergeType,
-                    genotypeMergeOption, true, printComplexMerges, ref.getBase(), SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC);
+            Map<VariantContext.Type, List<VariantContext>> VCsByType = VariantContextUtils.separateVariantContextsByType(vcs);
+            // iterate over the keys (and not the values) so that it's deterministic
+            for ( VariantContext.Type type : VCsByType.keySet() ) {
+                mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), VCsByType.get(type),
+                        priority, filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
+                        ref.getBase(), SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
+            }
         }
 
-        //out.printf("   merged => %s%nannotated => %s%n", mergedVC, annotatedMergedVC);
+        for ( VariantContext mergedVC : mergedVCs ) {
+            // only operate at the start of events
+            if ( mergedVC == null )
+                continue;
 
-        if ( mergedVC != null ) { // only operate at the start of events
             HashMap<String, Object> attributes = new HashMap<String, Object>(mergedVC.getAttributes());
             // re-compute chromosome counts
             VariantContextUtils.calculateChromosomeCounts(mergedVC, attributes, false);
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index c1eb48b68..212600360 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -492,7 +492,7 @@ public class VariantContextUtils {
             if ( ! filteredAreUncalled || vc.isNotFiltered() )
                 VCs.add(VariantContext.createVariantContextWithPaddedAlleles(vc,inputRefBase,false));
         }
-        if ( VCs.size() == 0 ) // everything is filtered out and we're filteredareUncalled
+        if ( VCs.size() == 0 ) // everything is filtered out and we're filteredAreUncalled
             return null;
 
         // establish the baseline info from the first VC
@@ -637,6 +637,17 @@ public class VariantContextUtils {
         return merged;
     }
 
+    public static Map<VariantContext.Type, List<VariantContext>> separateVariantContextsByType(Collection<VariantContext> VCs) {
+        HashMap<VariantContext.Type, List<VariantContext>> mappedVCs = new HashMap<VariantContext.Type, List<VariantContext>>();
+        for ( VariantContext vc : VCs ) {
+            if ( !mappedVCs.containsKey(vc.getType()) )
+                mappedVCs.put(vc.getType(), new ArrayList<VariantContext>());
+            mappedVCs.get(vc.getType()).add(vc);
+        }
+
+        return mappedVCs;
+    }
+
     private static class AlleleMapper {
         private VariantContext vc = null;
         private Map<Allele, Allele> map = null;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
index 00ee44f75..c5fd9bcbe 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -80,9 +80,9 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
 
     @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "1d5a021387a8a86554db45a29f66140f", false); } // official project VCF files in tabix format
     @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "20163d60f18a46496f6da744ab5cc0f9", false); } // official project VCF files in tabix format
-    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "5b82f37df1f5ba40f0474d71c94142ec", false); }
+    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "cba8f749f2444d69a54553b15328ed47", false); }
 
-    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "c58dca482bf97069eac6d9f1a07a2cba", false); }
+    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "78b169cf9955c9fd01340292d5ba2dca", false); }
 
     @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "89f55abea8f59e39d1effb908440548c", true); }
 
@@ -100,7 +100,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                         " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
                         " -genotypeMergeOptions UNIQUIFY -L 1"),
                 1,
-                Arrays.asList("8b78339ccf7a5a5a837f79e88a3a38e5"));
+                Arrays.asList("0e475c98d5152fb12eb17f3907b849a9"));
         executeTest("threeWayWithRefs", spec);
     }