diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
index 507a6559c..97a4ac468 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
@@ -22,12 +22,12 @@ public class BaseQualityRankSumTest extends RankSumTest {
 
     public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseQRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities")); }
 
-    protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
+    protected void fillQualsFromPileup(byte ref, List<Byte> alts, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
         for ( final PileupElement p : pileup ) {
             if( isUsableBase(p) ) {
                 if ( p.getBase() == ref )
                     refQuals.add((double)p.getQual());
-                else if ( p.getBase() == alt )
+                else if ( alts.contains(p.getBase()) )
                     altQuals.add((double)p.getQual());
             }
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
index 9857c339f..aa4f26ef3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
@@ -24,12 +24,12 @@ public class MappingQualityRankSumTest extends RankSumTest {
 
     public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("MQRankSum", 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities")); }
 
-    protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
+    protected void fillQualsFromPileup(byte ref, List<Byte> alts, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
         for ( final PileupElement p : pileup ) {
             if ( isUsableBase(p) ) {
                 if ( p.getBase() == ref ) {
                     refQuals.add((double)p.getMappingQual());
-                } else if ( p.getBase() == alt ) {
+                } else if ( alts.contains(p.getBase()) ) {
                     altQuals.add((double)p.getMappingQual());
                 }
             }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index e0e62cdb0..3f555f780 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -12,6 +12,7 @@ import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -41,16 +42,19 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
         final ArrayList<Double> refQuals = new ArrayList<Double>();
         final ArrayList<Double> altQuals = new ArrayList<Double>();
 
-        if (vc.isSNP() && vc.isBiallelic()) {
-            // todo - no current support for multiallelic snps
-            for (final Genotype genotype : genotypes.iterateInSampleNameOrder()) {
+        if ( vc.isSNP() ) {
+            for ( final Genotype genotype : genotypes.iterateInSampleNameOrder() ) {
                 final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
-                if (context == null) {
+                if ( context == null )
                     continue;
-                }
-                fillQualsFromPileup(ref.getBase(), vc.getAlternateAllele(0).getBases()[0], context.getBasePileup(), refQuals, altQuals);
+
+                final List<Byte> altAlleles = new ArrayList<Byte>();
+                for ( final Allele a : vc.getAlternateAlleles() )
+                    altAlleles.add(a.getBases()[0]);
+                
+                fillQualsFromPileup(ref.getBase(), altAlleles, context.getBasePileup(), refQuals, altQuals);
             }
-        } else if (vc.isIndel() || vc.isMixed()) {
+        } else if ( vc.isIndel() || vc.isMixed() ) {
 
             for (final Genotype genotype : genotypes.iterateInSampleNameOrder()) {
                 final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
@@ -105,7 +109,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
 
     }
 
-    protected abstract void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals);
+    protected abstract void fillQualsFromPileup(byte ref, List<Byte> alts, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals);
 
     protected abstract void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals);
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
index b0039d1a0..a998cd08b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
@@ -32,7 +32,7 @@ public class ReadPosRankSumTest extends RankSumTest {
         return Arrays.asList(new VCFInfoHeaderLine("ReadPosRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"));
     }
 
-    protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
+    protected void fillQualsFromPileup(byte ref, List<Byte> alts, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
         for (final PileupElement p : pileup) {
             if (isUsableBase(p)) {
                 int readPos = AlignmentUtils.calcAlignmentByteArrayOffset(p.getRead().getCigar(), p, 0, 0);
@@ -41,11 +41,10 @@ public class ReadPosRankSumTest extends RankSumTest {
                     readPos = numAlignedBases - (readPos + 1);
 
 
-                if (p.getBase() == ref)
+                if ( p.getBase() == ref )
                     refQuals.add((double) readPos);
-                else if (p.getBase() == alt)
+                else if ( alts.contains(p.getBase()) )
                     altQuals.add((double) readPos);
-
             }
         }
     }