diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
index 0644c669b..0de405d97 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
@@ -154,10 +154,10 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
         try {
             switch( type ) {
                 case ALL:
-                    vc.extraStrictValidation(observedRefAllele, rsIDs);
+                    vc.extraStrictValidation(observedRefAllele, ref.getBase(), rsIDs);
                     break;
                 case REF:
-                    vc.validateReferenceBases(observedRefAllele);
+                    vc.validateReferenceBases(observedRefAllele, ref.getBase());
                     break;
                 case IDS:
                     vc.validateRSIDs(rsIDs);
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 1712f6f7b..fff1961c6 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1055,11 +1055,12 @@ public class VariantContext implements Feature { // to enable tribble intergrati
      * Run all extra-strict validation tests on a Variant Context object
      *
      * @param reference        the true reference allele
+     * @param paddedRefBase    the reference base used for padding indels
      * @param rsIDs            the true dbSNP IDs
      */
-    public void extraStrictValidation(Allele reference, Set<String> rsIDs) {
+    public void extraStrictValidation(Allele reference, Byte paddedRefBase, Set<String> rsIDs) {
         // validate the reference
-        validateReferenceBases(reference);
+        validateReferenceBases(reference, paddedRefBase);
 
         // validate the RS IDs
         validateRSIDs(rsIDs);
@@ -1074,11 +1075,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         //checkReferenceTrack();
     }
 
-    public void validateReferenceBases(Allele reference) {
+    public void validateReferenceBases(Allele reference, Byte paddedRefBase) {
         // don't validate if we're an insertion
         if ( !reference.isNull() && !reference.basesMatch(getReference()) ) {
             throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
         }
+
+        // we also need to validate the padding base for simple indels
+        if ( hasReferenceBaseForIndel() && !getReferenceBaseForIndel().equals(paddedRefBase) )
+            throw new TribbleException.InternalCodecException(String.format("the padded REF base is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), (char)getReferenceBaseForIndel().byteValue(), (char)paddedRefBase.byteValue()));
     }
 
     public void validateRSIDs(Set<String> rsIDs) {