diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java
index 4d071a0ee..63395707a 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java
@@ -52,23 +52,30 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
 		this.parseHeader();
 	}
 
-	private void parseHeader()
-	{
+	/**
+     * parse the header from the top of the file.  We read lines that match
+     * the header pattern, and try to create a header.  We then create the first
+     * record from the first non-header line in the file.
+     */
+    private void parseHeader() {
         String line = null;
         // try and parse the header
         try {
             ArrayList<String> lines = new ArrayList<String>();
             line = mReader.readLine();
-            while (line.startsWith("#")) {
+            while (line != null && line.startsWith("#")) {
                 lines.add(line);
                 line = mReader.readLine();
             }
+            // try to make a header from the lines we parsed
             mHeader = this.createHeader(lines);
-            mNextRecord = createRecord(line, mHeader);
+
+            // if the last line we parsed is null, we shouldn't try to make a record of it
+            if (line != null) mNextRecord = createRecord(line, mHeader);
         } catch (IOException e) {
             throw new RuntimeException("VCFReader: Failed to parse VCF File on line: " + line, e);
         }
-	}
+    }
 
     /**
      * open a g-zipped version of the VCF format
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java
index 0203868c8..1e9c8f608 100644
--- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java
+++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java
@@ -22,7 +22,8 @@ public class VCFReaderTest extends BaseTest {
     private static final File multiSampleVCF = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/MultiSample.vcf");
     private static final String VCF_MIXUP_FILE = "/humgen/gsa-scr1/GATK_Data/Validation_Data/mixedup.v2.vcf";
     private static final File complexFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/complexExample.vcf");
-
+    private static final File headerNoRecordsFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/headerNoRecords.vcf");
+    
     private static IndexedFastaSequenceFile seq;
 
        @BeforeClass
@@ -325,4 +326,12 @@ public class VCFReaderTest extends BaseTest {
 
         if (reader.hasNext()) Assert.fail("The reader should NOT have a record");
     }
+
+    public void testHeaderNoRecords() {
+        VCFReader reader = new VCFReader(headerNoRecordsFile);
+        Assert.assertTrue(reader.getHeader().getMetaData() != null);
+        Iterator<VCFRecord> iter = reader.iterator();
+        Assert.assertTrue(!reader.iterator().hasNext());
+
+    }
 }