diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 567262756..3d14308b6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -579,6 +579,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     }
 
     private boolean badIndelSize(final VariantContext vc) {
+        List<Integer> lengths = vc.getIndelLengths();
+        if ( lengths == null )
+            return false; // VC does not harbor indel
         for ( Integer indelLength : vc.getIndelLengths() ) {
             if ( indelLength > maxIndelSize )
                 return true;
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 8da6d452e..929e53ce7 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -716,7 +716,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
      * @return a list of indel lengths ( null if not of type indel or mixed )
      */
     public List<Integer> getIndelLengths() {
-        if ( getType() != Type.INDEL && getType() != Type.MIXED ) {
+        if ( getType() != Type.INDEL && getType() != Type.MIXED && getType() != Type.STRUCTURAL_INDEL ) {
             return null;
         }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index bde597fbe..77e29f87b 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -128,6 +128,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         executeTest("testVariantTypeSelection--" + testFile, spec);
     }
 
+    @Test
+    public void testIndelLengthSelection() {
+        String testFile = privateTestDir + "complexExample1.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants -R " + b36KGReference + " -selectType INDEL --variant " + testFile + " -o %s --no_cmdline_in_header --maxIndelSize 3",
+                1,
+                Arrays.asList("004589868ca5dc887e2dff876b4cc797")
+        );
+
+        executeTest("testIndelLengthSelection--" + testFile, spec);
+    }
+
     @Test
     public void testUsingDbsnpName() {
         String testFile = privateTestDir + "combine.3.vcf";