diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
index ad77615bc..2b51e6776 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -95,6 +95,7 @@ import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.vcf.*;
+import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants;
 
 import java.io.FileNotFoundException;
 import java.io.PrintStream;
@@ -614,6 +615,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     public void initialize() {
         super.initialize();
 
+        if (SCAC.genotypeArgs.samplePloidy != HomoSapiensConstants.DEFAULT_PLOIDY)
+            throw new UserException.BadArgumentValue("-ploidy", "" + SCAC.genotypeArgs.samplePloidy + "; currently HaplotypeCaller only supports diploid sample analysis (-ploidy 2)");
+
         if (dontGenotype && emitReferenceConfidence())
             throw new UserException("You cannot request gVCF output and do not genotype at the same time");