Index: lucene/CHANGES.txt
===================================================================
--- lucene/CHANGES.txt	(revision 1398854)
+++ lucene/CHANGES.txt	(working copy)
@@ -57,6 +57,9 @@
 * LUCENE-4468: Fix rareish integer overflows in Block and Lucene40 postings 
   formats (Robert Muir)
 
+* LUCENE-4485: When CheckIndex terms, terms/docs pairs and tokens,
+  these counts now all exclude deleted documents.  (Mike McCandless)
+
 Optimizations
 
 * LUCENE-4443: BlockPostingsFormat no longer writes unnecessary offsets 
Index: lucene/core/src/test/org/apache/lucene/index/TestCheckIndex.java
===================================================================
--- lucene/core/src/test/org/apache/lucene/index/TestCheckIndex.java	(revision 1398854)
+++ lucene/core/src/test/org/apache/lucene/index/TestCheckIndex.java	(working copy)
@@ -75,8 +75,8 @@
 
     assertNotNull(seg.termIndexStatus);
     assertNull(seg.termIndexStatus.error);
-    assertEquals(19, seg.termIndexStatus.termCount);
-    assertEquals(19, seg.termIndexStatus.totFreq);
+    assertEquals(18, seg.termIndexStatus.termCount);
+    assertEquals(18, seg.termIndexStatus.totFreq);
     assertEquals(18, seg.termIndexStatus.totPos);
 
     assertNotNull(seg.storedFieldStatus);
Index: lucene/core/src/java/org/apache/lucene/index/CheckIndex.java
===================================================================
--- lucene/core/src/java/org/apache/lucene/index/CheckIndex.java	(revision 1398854)
+++ lucene/core/src/java/org/apache/lucene/index/CheckIndex.java	(working copy)
@@ -233,9 +233,12 @@
       TermIndexStatus() {
       }
 
-      /** Total term count */
+      /** Number of terms with at least one live doc. */
       public long termCount = 0L;
 
+      /** Number of terms with zero live docs docs. */
+      public long delTermCount = 0L;
+
       /** Total frequency across all terms. */
       public long totFreq = 0L;
       
@@ -750,7 +753,7 @@
       final TermsEnum termsEnum = terms.iterator(null);
       
       boolean hasOrd = true;
-      final long termCountStart = status.termCount;
+      final long termCountStart = status.delTermCount + status.termCount;
       
       BytesRef lastTerm = null;
       
@@ -781,7 +784,6 @@
         if (docFreq <= 0) {
           throw new RuntimeException("docfreq: " + docFreq + " is out of bounds");
         }
-        status.totFreq += docFreq;
         sumDocFreq += docFreq;
         
         docs = termsEnum.docs(liveDocs, docs);
@@ -796,15 +798,13 @@
           }
           
           if (hasOrd) {
-            final long ordExpected = status.termCount - termCountStart;
+            final long ordExpected = status.delTermCount + status.termCount - termCountStart;
             if (ord != ordExpected) {
               throw new RuntimeException("ord mismatch: TermsEnum has ord=" + ord + " vs actual=" + ordExpected);
             }
           }
         }
         
-        status.termCount++;
-        
         final DocsEnum docs2;
         if (postings != null) {
           docs2 = postings;
@@ -820,6 +820,7 @@
           if (doc == DocIdSetIterator.NO_MORE_DOCS) {
             break;
           }
+          status.totFreq++;
           visitedDocs.set(doc);
           int freq = -1;
           if (hasFreqs) {
@@ -883,6 +884,12 @@
           }
         }
         
+        if (docCount != 0) {
+          status.termCount++;
+        } else {
+          status.delTermCount++;
+        }
+        
         final long totalTermFreq2 = termsEnum.totalTermFreq();
         final boolean hasTotalTermFreq = hasFreqs && totalTermFreq2 != -1;
         
@@ -1063,11 +1070,11 @@
         // check unique term count
         long termCount = -1;
         
-        if (status.termCount-termCountStart > 0) {
+        if ((status.delTermCount+status.termCount)-termCountStart > 0) {
           termCount = fields.terms(field).size();
           
-          if (termCount != -1 && termCount != status.termCount - termCountStart) {
-            throw new RuntimeException("termCount mismatch " + termCount + " vs " + (status.termCount - termCountStart));
+          if (termCount != -1 && termCount != status.delTermCount + status.termCount - termCountStart) {
+            throw new RuntimeException("termCount mismatch " + (status.delTermCount + termCount) + " vs " + (status.termCount - termCountStart));
           }
         }