diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index 303a2871a..4b1483cb6 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -144,7 +144,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
     }
 
     @Test
-    public void testSampleExclusion() {
+    public void testSampleExclusionFromFileAndSeparateSample() {
         String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
         String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
 
@@ -158,6 +158,21 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         executeTest("testSampleExclusion--" + testfile, spec);
     }
 
+    @Test
+    public void testSampleExclusionJustFromFile() {
+        String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
+        String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sf " + samplesFile + " --variant " + testfile,
+                1,
+                Arrays.asList("875d7e00ac8081e87ab9fb1b20c83677")
+        );
+        spec.disableShadowBCF();
+
+        executeTest("testSampleExclusion--" + testfile, spec);
+    }
+
     @Test
     public void testSampleInclusionWithNonexistingSamples() {
         String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
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 02c8ed8d8..1f2b6d09b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -377,10 +377,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         }
 
         // now, exclude any requested samples
-        Collection<String> XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles);
+        final Collection<String> XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles);
         samples.removeAll(XLsamplesFromFile);
         samples.removeAll(XLsampleNames);
-        NO_SAMPLES_SPECIFIED = NO_SAMPLES_SPECIFIED && XLsampleNames.isEmpty();
+        NO_SAMPLES_SPECIFIED = NO_SAMPLES_SPECIFIED && XLsampleNames.isEmpty() && XLsamplesFromFile.isEmpty();
 
         if ( samples.size() == 0 && !NO_SAMPLES_SPECIFIED )
             throw new UserException("All samples requested to be included were also requested to be excluded.");