diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index d82d920a8..5866075a7 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -226,15 +226,29 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     }
 
     @Test
-    public void testSnpEffAnnotationsUnsupportedVersion() {
+    public void testSnpEffAnnotationsUnsupportedVersionGATKMode() {
         WalkerTestSpec spec = new WalkerTestSpec(
-            "-T VariantAnnotator -R " + hg19Reference + " --no_cmdline_in_header -o %s -A SnpEff --variant " +
-            validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile  " + validationDataLocation +
-            "snpEff.AFR.unfiltered.unsupported.version.vcf -L 1:1-1,500,000",
+            "-T VariantAnnotator -R " + b37KGReference + " --no_cmdline_in_header -o %s -A SnpEff " +
+            "--variant " + privateTestDir + "vcf4.1.example.vcf " +
+            "--snpEffFile  " + privateTestDir + "snpEff_unsupported_version_gatk_mode.vcf " +
+            "-L 1:10001292-10012424",
+            1,
+            Arrays.asList("7352cf23a4d45d3d2bb34ab44a4100ae")
+        );
+        executeTest("Testing SnpEff annotations (unsupported version, GATK mode)", spec);
+    }
+
+    @Test
+    public void testSnpEffAnnotationsUnsupportedVersionNoGATKMode() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+            "-T VariantAnnotator -R " + b37KGReference + " --no_cmdline_in_header -o %s -A SnpEff " +
+            "--variant " + privateTestDir + "vcf4.1.example.vcf " +
+            "--snpEffFile  " + privateTestDir + "snpEff_unsupported_version_no_gatk_mode.vcf " +
+            "-L 1:10001292-10012424",
             1,
             UserException.class
         );
-        executeTest("Testing SnpEff annotations (unsupported version)", spec);
+        executeTest("Testing SnpEff annotations (unsupported version, no GATK mode)", spec);
     }
 
     @Test
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
index bc365c59c..288196d1b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
@@ -42,6 +42,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
+import java.util.regex.Pattern;
 
 /**
  * A set of genomic annotations based on the output of the SnpEff variant effect predictor tool
@@ -63,6 +64,8 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
     public static final String[] SUPPORTED_SNPEFF_VERSIONS = { "2.0.5" };
     public static final String SNPEFF_VCF_HEADER_VERSION_LINE_KEY = "SnpEffVersion";
     public static final String SNPEFF_VCF_HEADER_COMMAND_LINE_KEY = "SnpEffCmd";
+    public static final String SNPEFF_GATK_COMPATIBILITY_ARGUMENT = "-o gatk";
+    public static final Pattern SNPEFF_GATK_COMPATIBILITY_ARGUMENT_PATTERN = Pattern.compile("-o\\s+gatk");
 
     // When we write the SnpEff version number and command line to the output VCF, we change
     // the key name slightly so that the output VCF won't be confused in the future for an
@@ -219,8 +222,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
         VCFHeaderLine snpEffVersionLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_VERSION_LINE_KEY);
         VCFHeaderLine snpEffCommandLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_COMMAND_LINE_KEY);
 
-        checkSnpEffVersion(snpEffVersionLine);
-        checkSnpEffCommandLine(snpEffCommandLine);
+        checkSnpEffVersionAndCommandLine(snpEffVersionLine, snpEffCommandLine);
 
         // If everything looks ok, add the SnpEff version number and command-line header lines to the
         // header of the VCF output file, changing the key names so that our output file won't be
@@ -267,37 +269,45 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
         }
     }
 
-    private void checkSnpEffVersion ( VCFHeaderLine snpEffVersionLine ) {
+    private void checkSnpEffVersionAndCommandLine( final VCFHeaderLine snpEffVersionLine, final VCFHeaderLine snpEffCommandLine ) {
         if ( snpEffVersionLine == null || snpEffVersionLine.getValue() == null || snpEffVersionLine.getValue().trim().length() == 0 ) {
-            throw new UserException("Could not find a " + SNPEFF_VCF_HEADER_VERSION_LINE_KEY + " entry in the VCF header for the SnpEff " +
-                                    "input file, and so could not verify that the file was generated by a supported version of SnpEff (" +
-                                    Arrays.toString(SUPPORTED_SNPEFF_VERSIONS) + ")");
+            throw new UserException(String.format("Could not find a %s entry in the VCF header for the SnpEff input file, " +
+                                                  "and so could not verify that the file was generated by a supported version of SnpEff (%s)",
+                                                  SNPEFF_VCF_HEADER_VERSION_LINE_KEY, supportedSnpEffVersionsString()));
+        }
+
+        if ( snpEffCommandLine == null || snpEffCommandLine.getValue() == null || snpEffCommandLine.getValue().trim().length() == 0 ) {
+            throw new UserException(String.format("Could not find a %s entry in the VCF header for the SnpEff input file, " +
+                                                  "which should be added by all supported versions of SnpEff (%s)",
+                                                  SNPEFF_VCF_HEADER_COMMAND_LINE_KEY, supportedSnpEffVersionsString()));
         }
 
         String snpEffVersionString = snpEffVersionLine.getValue().replaceAll("\"", "").split(" ")[0];
 
-        if ( ! isSupportedSnpEffVersion(snpEffVersionString) ) {
-            throw new UserException("The version of SnpEff used to generate the SnpEff input file (" + snpEffVersionString + ") " +
-                                    "is not currently supported by the GATK. Supported versions are: " + Arrays.toString(SUPPORTED_SNPEFF_VERSIONS));
+        if ( ! isSupportedSnpEffVersion(snpEffVersionString, snpEffCommandLine.getValue()) ) {
+            throw new UserException(String.format("The version of SnpEff used to generate the SnpEff input file (%s) " +
+                                                  "is not currently supported by the GATK, and was not run in GATK " +
+                                                  "compatibility mode. Supported versions are: %s",
+                                                  snpEffVersionString, supportedSnpEffVersionsString()));
         }
     }
 
-    private void checkSnpEffCommandLine ( VCFHeaderLine snpEffCommandLine ) {
-        if ( snpEffCommandLine == null || snpEffCommandLine.getValue() == null || snpEffCommandLine.getValue().trim().length() == 0 ) {
-            throw new UserException("Could not find a " + SNPEFF_VCF_HEADER_COMMAND_LINE_KEY + " entry in the VCF header for the SnpEff " +
-                                    "input file, which should be added by all supported versions of SnpEff (" +
-                                    Arrays.toString(SUPPORTED_SNPEFF_VERSIONS) + ")");
-        }
-    }
-
-    private boolean isSupportedSnpEffVersion ( String versionString ) {
+    private boolean isSupportedSnpEffVersion( final String versionString, final String commandLine ) {
+        // first check to see if it's an officially-supported version
         for ( String supportedVersion : SUPPORTED_SNPEFF_VERSIONS ) {
             if ( supportedVersion.equals(versionString) ) {
                 return true;
             }
         }
 
-        return false;
+        // if it's not an officially-supported version, check to see whether the
+        // "-o gatk" compatibility option was specified
+        return SNPEFF_GATK_COMPATIBILITY_ARGUMENT_PATTERN.matcher(commandLine).find();
+    }
+
+    private String supportedSnpEffVersionsString() {
+        return String.format("%s, as well as later versions when run with the option %s",
+                             Arrays.toString(SUPPORTED_SNPEFF_VERSIONS), SNPEFF_GATK_COMPATIBILITY_ARGUMENT);
     }
 
     private VariantContext getMatchingSnpEffRecord ( List<VariantContext> snpEffRecords, VariantContext vc ) {