diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index 1749a13cf..3e581be05 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -97,7 +97,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
             vc = VariantContext.modifyLocation(vc, toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length);
             VariantContext newVC = VariantContext.createVariantContextWithPaddedAlleles(vc, ref.getBase(), false);
 
-            if ( originalVC.isSNP() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) {
+            if ( originalVC.isSNP() && originalVC.isBiallelic() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) {
                 logger.warn(String.format("VCF at %s / %d => %s / %d is switching substitution type %s/%s to %s/%s",
                         originalVC.getChr(), originalVC.getStart(), newVC.getChr(), newVC.getStart(),
                         originalVC.getReference(), originalVC.getAlternateAllele(0), newVC.getReference(), newVC.getAlternateAllele(0)));