diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
index 0f2353ce5..366e927dc 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
@@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.filters;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceRecord;
+import net.sf.samtools.SAMTagUtil;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -59,9 +60,14 @@ public class MalformedReadFilter extends ReadFilter {
                 !checkCigarDisagreesWithAlignment(read);
     }
 
-    private static boolean checkHasReadGroup(SAMRecord read) {
-        if ( read.getReadGroup() == null )
-            throw new UserException.ReadMissingReadGroup(read);
+    private static boolean checkHasReadGroup(final SAMRecord read) {
+        if ( read.getReadGroup() == null ) {
+            // there are 2 possibilities: either the RG tag is missing or it is not defined in the header
+            final String rgID = (String)read.getAttribute(SAMTagUtil.getSingleton().RG);
+            if ( rgID == null )
+                throw new UserException.ReadMissingReadGroup(read);
+            throw new UserException.ReadHasUndefinedReadGroup(read, rgID);
+        }
         return true;
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index 5c67c899c..0c01539d4 100644
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -276,8 +276,14 @@ public class UserException extends ReviewedStingException {
     }
 
     public static class ReadMissingReadGroup extends MalformedBAM {
-        public ReadMissingReadGroup(SAMRecord read) {
-            super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK.  Please use " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName()));
+        public ReadMissingReadGroup(final SAMRecord read) {
+            super(read, String.format("Read %s is missing the read group (RG) tag, which is required by the GATK.  Please use " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName()));
+        }
+    }
+
+    public static class ReadHasUndefinedReadGroup extends MalformedBAM {
+        public ReadHasUndefinedReadGroup(final SAMRecord read, final String rgID) {
+            super(read, String.format("Read %s uses a read group (%s) that is not defined in the BAM header, which is not valid.  Please use " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName(), rgID));
         }
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/filters/BadReadGroupsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/filters/BadReadGroupsIntegrationTest.java
new file mode 100644
index 000000000..12d875a4d
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/filters/BadReadGroupsIntegrationTest.java
@@ -0,0 +1,52 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.sting.gatk.filters;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.testng.annotations.Test;
+
+
+public class BadReadGroupsIntegrationTest extends WalkerTest {
+
+    @Test
+    public void testMissingReadGroup() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T PrintReads -R " + b36KGReference + " -I " + privateTestDir + "missingReadGroup.bam -o /dev/null",
+                0,
+                UserException.ReadMissingReadGroup.class);
+        executeTest("test Missing Read Group", spec);
+    }
+
+    @Test
+    public void testUndefinedReadGroup() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T PrintReads -R " + b36KGReference + " -I " + privateTestDir + "undefinedReadGroup.bam -o /dev/null",
+                0,
+                UserException.ReadHasUndefinedReadGroup.class);
+        executeTest("test Undefined Read Group", spec);
+    }
+}