diff --git a/pmd-matlab/etc/grammar/matlab.jj b/pmd-matlab/etc/grammar/matlab.jj
index 35dbc8625d..6f61dd0d42 100644
--- a/pmd-matlab/etc/grammar/matlab.jj
+++ b/pmd-matlab/etc/grammar/matlab.jj
@@ -39,27 +39,19 @@ PARSER_END(MatlabParser)
   "\r\n" : DEFAULT
 |
   "\n" : DEFAULT
-|
-  "%{"  : IN_COMMENT
-|
-  "%" : IN_LINE_COMMENT
-
 }
 
-<IN_COMMENT> SKIP:
-{
-    "%}" : DEFAULT
-}
+MORE:
+{ "%{": IN_COMMENT }
 
-<IN_LINE_COMMENT> SKIP:
-{
-   "\n" : DEFAULT
-}
+SPECIAL_TOKEN:
+{ <SINGLE_LINE_COMMENT: "%"(~["\n","\r"])* ("\n"|"\r"|"\r\n")?> }
 
-<IN_LINE_COMMENT, IN_COMMENT> MORE:
-{
-    < ~[] >
-}
+<IN_COMMENT> SPECIAL_TOKEN:
+{ <MULTI_LINE_COMMENT: "%}">: DEFAULT }
+
+<IN_COMMENT> MORE:
+{ < ~[] > }
 
 <DEFAULT, TRANSPOSE> TOKEN : /* SEPARATORS AND OTHER USEFULL LANGUAGE CONSTRUCTS*/
 {
diff --git a/pmd-matlab/src/main/java/net/sourceforge/pmd/cpd/MatlabTokenizer.java b/pmd-matlab/src/main/java/net/sourceforge/pmd/cpd/MatlabTokenizer.java
index b2157bd043..4b135d1be7 100644
--- a/pmd-matlab/src/main/java/net/sourceforge/pmd/cpd/MatlabTokenizer.java
+++ b/pmd-matlab/src/main/java/net/sourceforge/pmd/cpd/MatlabTokenizer.java
@@ -9,9 +9,10 @@ import java.io.StringReader;
 
 import org.apache.commons.io.IOUtils;
 
+import net.sourceforge.pmd.cpd.token.JavaCCTokenFilter;
+import net.sourceforge.pmd.cpd.token.TokenFilter;
 import net.sourceforge.pmd.lang.LanguageRegistry;
 import net.sourceforge.pmd.lang.LanguageVersionHandler;
-import net.sourceforge.pmd.lang.TokenManager;
 import net.sourceforge.pmd.lang.ast.TokenMgrError;
 import net.sourceforge.pmd.lang.matlab.MatlabLanguageModule;
 import net.sourceforge.pmd.lang.matlab.ast.Token;
@@ -31,13 +32,13 @@ public class MatlabTokenizer implements Tokenizer {
                     .getDefaultVersion().getLanguageVersionHandler();
             reader = new StringReader(buffer.toString());
             reader = IOUtil.skipBOM(reader);
-            TokenManager tokenManager = languageVersionHandler
+            final TokenFilter tokenFilter = new JavaCCTokenFilter(languageVersionHandler
                     .getParser(languageVersionHandler.getDefaultParserOptions())
-                    .getTokenManager(sourceCode.getFileName(), reader);
-            Token currentToken = (Token) tokenManager.getNextToken();
-            while (currentToken.image.length() > 0) {
+                    .getTokenManager(sourceCode.getFileName(), reader));
+            Token currentToken = (Token) tokenFilter.getNextToken();
+            while (currentToken != null) {
                 tokenEntries.add(new TokenEntry(currentToken.image, sourceCode.getFileName(), currentToken.beginLine));
-                currentToken = (Token) tokenManager.getNextToken();
+                currentToken = (Token) tokenFilter.getNextToken();
             }
             tokenEntries.add(TokenEntry.getEOF());
             System.err.println("Added " + sourceCode.getFileName());
diff --git a/pmd-matlab/src/test/java/net/sourceforge/pmd/cpd/MatlabTokenizerTest.java b/pmd-matlab/src/test/java/net/sourceforge/pmd/cpd/MatlabTokenizerTest.java
index e2ce74f064..0557063eb0 100644
--- a/pmd-matlab/src/test/java/net/sourceforge/pmd/cpd/MatlabTokenizerTest.java
+++ b/pmd-matlab/src/test/java/net/sourceforge/pmd/cpd/MatlabTokenizerTest.java
@@ -4,12 +4,15 @@
 
 package net.sourceforge.pmd.cpd;
 
+import static org.junit.Assert.assertEquals;
+
 import java.io.IOException;
 
 import org.apache.commons.io.IOUtils;
 import org.junit.Before;
 import org.junit.Test;
 
+import net.sourceforge.pmd.PMD;
 import net.sourceforge.pmd.testframework.AbstractTokenizerTest;
 
 public class MatlabTokenizerTest extends AbstractTokenizerTest {
@@ -33,4 +36,21 @@ public class MatlabTokenizerTest extends AbstractTokenizerTest {
         this.expectedTokenCount = 3925;
         super.tokenizeTest();
     }
+    
+    @Test
+    public void testIgnoreBetweenSpecialComments() throws IOException {
+        SourceCode sourceCode = new SourceCode(new SourceCode.StringCodeLoader("% CPD-OFF" + PMD.EOL
+                + "function g = vec(op, y)" + PMD.EOL
+                + "  opy = op(y);" + PMD.EOL
+                + "  if ( any(size(opy) > 1) )" + PMD.EOL
+                + "    g = @loopWrapperArray;" + PMD.EOL
+                + "  end" + PMD.EOL
+                + "  % CPD-ON" + PMD.EOL
+                + "end"
+        ));
+        Tokens tokens = new Tokens();
+        tokenizer.tokenize(sourceCode, tokens);
+        TokenEntry.getEOF();
+        assertEquals(2, tokens.size()); // 2 tokens: "end" + EOF
+    }
 }