diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
index aaa2e63a7..b3329c708 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
@@ -120,6 +120,8 @@ public class VCF3Codec extends AbstractVCFCodec {
             genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
 
         int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
+        if ( nParts != genotypeParts.length )
+            generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records", lineNo);
 
         ArrayList<Genotype> genotypes = new ArrayList<Genotype>(nParts);
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
index 4c1bb1d9e..453155be7 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
@@ -147,6 +147,8 @@ public class VCFCodec extends AbstractVCFCodec {
             genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
 
         int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
+        if ( nParts != genotypeParts.length )
+            generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records", lineNo);
 
         ArrayList<Genotype> genotypes = new ArrayList<Genotype>(nParts);