diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountFunctionalClasses.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountFunctionalClasses.java
new file mode 100755
index 000000000..ff319a7f2
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountFunctionalClasses.java
@@ -0,0 +1,77 @@
+package org.broadinstitute.sting.gatk.walkers.varianteval;
+
+import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
+import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+
+@Analysis(name = "Count Functional Classes", description = "Counts instances of different functional variant classes (provided the variants are annotated with that information)")
+public class CountFunctionalClasses extends VariantEvaluator {
+    // the following fields are in output order:
+    @DataPoint(description = "miRNA")
+    long nMiRNA= 0;
+
+    @DataPoint(description = "3'-UTR")
+    long nUTR3 = 0;
+
+    @DataPoint(description = "Intron")
+    long nIntron = 0;
+
+    @DataPoint(description = "Splice-site")
+    long nSpliceSite= 0;
+
+    @DataPoint(description = "Read-through")
+    long nReadThrough = 0;
+
+    @DataPoint(description = "Nonsense")
+    long nNonsense = 0;
+
+    @DataPoint(description = "Missense")
+    long nMissense = 0;
+
+    @DataPoint(description = "Synonymous")
+    long nSynonymous = 0;
+
+    @DataPoint(description = "5'-UTR")
+    long nUTR5= 0;
+
+    @DataPoint(description = "Promoter")
+    long nPromoter = 0;
+
+    public CountFunctionalClasses(VariantEvalWalker parent) {
+        super(parent);
+    }
+
+    public String getName() {
+        return "functionalclasses";
+    }
+
+    public boolean enabled() {
+        return false;
+    }
+
+    public int getComparisonOrder() {
+        return 1;
+    }
+
+    public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        String type = vc1.getAttributeAsString("type");
+
+        if (type != null) {
+            if      (type.equalsIgnoreCase("miRNA")) { nMiRNA++; }
+            else if (type.equalsIgnoreCase("3'-UTR")) { nUTR3++; }
+            else if (type.equalsIgnoreCase("Intron")) { nIntron++; }
+            else if (type.equalsIgnoreCase("Splice_site")) { nSpliceSite++; }
+            else if (type.equalsIgnoreCase("Read-through")) { nReadThrough++; }
+            else if (type.equalsIgnoreCase("Nonsense")) { nNonsense++; }
+            else if (type.equalsIgnoreCase("Missense")) { nMissense++; }
+            else if (type.equalsIgnoreCase("Synonymous")) { nSynonymous++; }
+            else if (type.equalsIgnoreCase("5'-UTR")) { nUTR5++; }
+            else if (type.equalsIgnoreCase("Promoter")) { nPromoter++; }
+        }
+
+        return null;
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 4f36ab524..fe184ea04 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -103,7 +103,7 @@ import java.util.*;
 
 
 /**
- * Test routine for new VariantContext object
+ * General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ts/Tv ratios, and a lot more)
  */
 @Reference(window=@Window(start=-50,stop=50))
 public class VariantEvalWalker extends RodWalker<Integer, Integer> {
@@ -389,6 +389,10 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     private List<EvaluationContext> initializeEvaluationContexts(Set<String> evalNames, Set<String> compNames, List<VariantContextUtils.JexlVCMatchExp> selectExps) {
         List<EvaluationContext> contexts = new ArrayList<EvaluationContext>();
 
+        // todo -- add another for loop for each sample (be smart about the selection here -
+        // honor specifications of just one or a few samples), and put an "all" in here so
+        // that we don't lose multi-sample evaluations
+
         selectExps = append(selectExps, null);
         for ( String evalName : evalNames ) {
             for ( String compName : compNames ) {
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 3cf9a4843..902a7d86e 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -97,6 +97,21 @@ public class
         }
     }
 
+    @Test
+    public void testVEGenomicallyAnnotated() {
+        String vecmd = "-T VariantEval " +
+                       "-R " + oneKGLocation + "reference/human_b36_both.fasta " +
+                       "-L 21 " +
+                       "-D " + GATKDataLocation + "dbsnp_129_b36.rod " +
+                       "-E CountFunctionalClasses " +
+                       "-B eval,VCF," + validationDataLocation + "test.filtered.maf_annotated.vcf " +
+                       "-o %s";
+        String md5 = "d41d8cd98f00b204e9800998ecf8427e";
+
+        WalkerTestSpec spec = new WalkerTestSpec(vecmd, 1, Arrays.asList(md5));
+        executeTest("testVEGenomicallyAnnotated", spec);
+    }
+
     @Test
     public void testVEWriteVCF() {
         String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30";