diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
index 32132c7ca..32002e093 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
@@ -96,24 +96,23 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
             loadArgumentsIntoObject(walker);
             argumentSources.add(walker);
 
-            Collection<RMDTriplet> newStyle = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser);
+            Collection<RMDTriplet> rodBindings = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser);
 
             // todo: remove me when the old style system is removed
             if ( getArgumentCollection().RODBindings.size() > 0 ) {
                 logger.warn("################################################################################");
                 logger.warn("################################################################################");
-                logger.warn("Deprecated -B rod binding syntax detected.  This syntax will be retired in GATK 1.2.");
+                logger.warn("Deprecated -B rod binding syntax detected.  This syntax has been eliminated in GATK 1.2.");
                 logger.warn("Please use arguments defined by each specific walker instead.");
                 for ( String oldStyleRodBinding : getArgumentCollection().RODBindings ) {
                     logger.warn("  -B rod binding with value " + oldStyleRodBinding + " tags: " + parser.getTags(oldStyleRodBinding).getPositionalTags());
                 }
                 logger.warn("################################################################################");
                 logger.warn("################################################################################");
+                System.exit(1);
             }
 
-            Collection<RMDTriplet> oldStyle = ListFileUtils.unpackRODBindingsOldStyle(getArgumentCollection().RODBindings, parser);
-            oldStyle.addAll(newStyle);
-            engine.setReferenceMetaDataFiles(oldStyle);
+            engine.setReferenceMetaDataFiles(rodBindings);
 
             for (ReadFilter filter: filters) {
                 loadArgumentsIntoObject(filter);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 62135f21b..fd39d46b0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -101,6 +101,8 @@ public class GATKArgumentCollection {
     @Input(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
     public File referenceFile = null;
 
+    @Deprecated
+    @Hidden
     @ElementList(required = false)
     @Input(fullName = "rodBind", shortName = "B", doc = "Bindings for reference-ordered data, in the form :<name>,<type> <file>", required = false)
     public ArrayList<String> RODBindings = new ArrayList<String>();
@@ -340,14 +342,6 @@ public class GATKArgumentCollection {
                 return false;
             }
         }
-        if (other.RODBindings.size() != RODBindings.size()) {
-            return false;
-        }
-        for (int x = 0; x < RODBindings.size(); x++) {
-            if (!RODBindings.get(x).equals(other.RODBindings.get(x))) {
-                return false;
-            }
-        }
         if (!other.samFiles.equals(this.samFiles)) {
             return false;
         }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java
index f3e868474..3a242cb13 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java
@@ -88,14 +88,6 @@ public class GATKArgumentCollectionUnitTest extends BaseTest {
         collect.intervals.add("intervals".toLowerCase());
         collect.excludeIntervals = new ArrayList<String>();
         collect.numberOfThreads = 1;
-
-        // make some rod bindings up
-        ArrayList<String> fakeBindings = new ArrayList<String>();
-        fakeBindings.add("Bind1");
-        fakeBindings.add("Bind2");
-        fakeBindings.add("Bind3");
-
-        collect.RODBindings = fakeBindings;
     }