diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java
index 69181df8c..1d4d497e1 100755
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java
@@ -216,6 +216,14 @@ class ArgumentDefinition {
         Class argumentType = sourceField.getType();
         return Collection.class.isAssignableFrom(argumentType) || sourceField.getType().isArray();         
     }
+
+    /**
+     * Is this argument a flag (meaning a boolean value whose presence indicates 'true').
+     * @return True if this argument is a flag.
+     */
+    public boolean isFlag() {
+        return (sourceField.getType() == Boolean.class) || (sourceField.getType() == Boolean.TYPE);
+    }
 }
 
 /**
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentMatches.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentMatches.java
index 6058c03f1..d45d1e64d 100755
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentMatches.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentMatches.java
@@ -177,12 +177,13 @@ class ArgumentMatch {
 
     /**
      * Does this argument already have a value at the given site?
-     * Arguments are only allowed to be single-valued.
+     * Arguments are only allowed to be single-valued per site, and
+     * flags aren't allowed a value at all.
      * @param index Index at which to check for values.
      * @return True if the argument has a value at the given site.  False otherwise.
      */
     public boolean hasValueAtSite( int index ) {
-        return indices.get(index) != null && indices.get(index).size() >= 1;
+        return (indices.get(index) != null && indices.get(index).size() >= 1) || isArgumentFlag();
     }
 
     /**
@@ -197,4 +198,12 @@ class ArgumentMatch {
         }
         return values;
     }
+
+    /**
+     * Convenience method returning true if the definition is a flag.
+     * @return True if definition is known to be a flag; false if not known to be a flag.
+     */
+    private boolean isArgumentFlag() {
+        return definition != null && definition.isFlag();    
+    }
 }
\ No newline at end of file
diff --git a/java/test/org/broadinstitute/sting/utils/cmdLine/ParsingEngineTest.java b/java/test/org/broadinstitute/sting/utils/cmdLine/ParsingEngineTest.java
index b8d03fe53..96a062a8d 100755
--- a/java/test/org/broadinstitute/sting/utils/cmdLine/ParsingEngineTest.java
+++ b/java/test/org/broadinstitute/sting/utils/cmdLine/ParsingEngineTest.java
@@ -345,4 +345,18 @@ public class ParsingEngineTest extends BaseTest {
         @Argument(doc="my arg")
         Integer myArg;
     }
+
+    @Test(expected=InvalidArgumentValueException.class)
+    public void booleanWithParameterTest() {
+        final String[] commandLine = new String[] {"--mybool", "true"};
+
+        parsingEngine.addArgumentSources( BooleanArgProvider.class );
+        ArgumentMatches argumentMatches = parsingEngine.parse( commandLine );
+        parsingEngine.validate(argumentMatches);
+    }
+
+    private class BooleanArgProvider {
+        @Argument(doc="my bool")
+        boolean myBool;
+    }
 }