diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
index 4f1e95499..7ea77a939 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -66,7 +66,8 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
     public boolean includeInDocs(ClassDoc doc) {
         try {
             Class type = HelpUtils.getClassForDoc(doc);
-            return JVMUtils.isConcrete(type);
+            boolean hidden = ! getDoclet().showHiddenFeatures() && type.isAnnotationPresent(Hidden.class);
+            return ! hidden && JVMUtils.isConcrete(type);
         } catch ( ClassNotFoundException e ) {
             return false;
         }