diff --git a/java/src/org/broad/tribble/vcf/VCFCompoundHeaderLine.java b/java/src/org/broad/tribble/vcf/VCFCompoundHeaderLine.java
index dff77e24d..e337791f8 100644
--- a/java/src/org/broad/tribble/vcf/VCFCompoundHeaderLine.java
+++ b/java/src/org/broad/tribble/vcf/VCFCompoundHeaderLine.java
@@ -137,15 +137,22 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
             return false;
         VCFCompoundHeaderLine other = (VCFCompoundHeaderLine)o;
         return name.equals(other.name) &&
-               count == other.count &&
-               description.equals(other.description) &&
-               type == other.type;
+                count == other.count &&
+                description.equals(other.description) &&
+                type == other.type &&
+                lineType == other.lineType;
     }
 
     public boolean equalsExcludingDescription(VCFCompoundHeaderLine other) {
         return count == other.count &&
-               type == other.type &&
-               name.equals(other.name);
+                type == other.type &&
+                lineType == other.lineType &&
+                name.equals(other.name);
+    }
+
+    public boolean sameLineTypeAndName(VCFCompoundHeaderLine other) {
+        return  lineType == other.lineType &&
+                name.equals(other.name);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index 671778b04..77e84768f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broad.tribble.vcf.VCFHeader;
 import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFCompoundHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
@@ -134,10 +135,14 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
             engine = new VariantAnnotatorEngine(getToolkit(), annotationGroupsToUse, annotationsToUse);
 
         // setup the header fields
+        // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
-        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), Arrays.asList("variant")));
-        hInfo.add(new VCFHeaderLine("source", "VariantAnnotator"));
         hInfo.addAll(engine.getVCFAnnotationDescriptions());
+        hInfo.add(new VCFHeaderLine("source", "VariantAnnotator"));
+        for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList("variant")) ) {
+            if ( isUniqueHeaderLine(line, hInfo) )
+                hInfo.add(line);
+        }
 
         vcfWriter = new VCFWriter(out);
         VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
@@ -148,6 +153,18 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
         }
     }
 
+    private static boolean isUniqueHeaderLine(VCFHeaderLine line, Set<VCFHeaderLine> currentSet) {
+        if ( !(line instanceof VCFCompoundHeaderLine) )
+            return true;
+
+        for ( VCFHeaderLine hLine : currentSet ) {
+            if ( hLine instanceof VCFCompoundHeaderLine && ((VCFCompoundHeaderLine)line).sameLineTypeAndName((VCFCompoundHeaderLine)hLine) )
+                return false;
+        }
+
+        return true;
+    }
+
     /**
      * Initialize the number of loci processed to zero.
      *
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 9c2a989e5..801da7cb3 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -75,6 +75,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
 
+    @Test
+    public void testOverwritingHeader() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
+                Arrays.asList("87d124ddfee8537e2052c495777d2b3b"));
+        executeTest("test overwriting header", spec);
+    }
+
     @Test
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(