diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
index 7111bac46..2e6a80462 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
@@ -104,6 +104,12 @@ public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
                     String sex = mVals.containsKey("sex") ? mVals.get("sex") : "3";
                     String pheno = mVals.get("phenotype");
                     outFam.printf("%s\t%s\t%s\t%s\t%s\t%s%n",fid,sample,pid,mid,sex,pheno);
+                } else {
+                    // even if a fam file is input, we can't diverge the bed file from the fam file, which
+                    // could lead to a malformed plink trio. Fail fast if there's any extra sample in the VCF.
+                    if ( ! sampleMetaValues.containsKey(sample) ) {
+                        throw new UserException("No metadata provided for sample "+sample);
+                    }
                 }
                 try {
                     File temp = File.createTempFile("VariantsToBPed_"+sample, ".tmp");
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java
index 07e82b869..a75da6cf9 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java
@@ -87,6 +87,31 @@ public class VariantsToBinaryPedIntegrationTest extends WalkerTest {
 
         executeTest(testName, spec);
     }
+
+    @Test
+    public void testFailFast() {
+        String testName = "testFailFast";
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString("HapMap.testFailFast.vcf", "HapMap_only_famids.fam",10),
+                3,
+                UserException.class
+        );
+
+        executeTest(testName, spec);
+    }
+
+    @Test
+    public void testFailFastMeta() {
+    String testName = "testFailFastMeta";
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString("HapMap.testFailFast.vcf", "HapMap_only_famids.metadata.txt",10),
+                3,
+                UserException.class
+        );
+
+        executeTest(testName, spec);
+
+    }
 }