diff --git a/index-common/src/main/java/com/metamx/druid/index/v1/IndexIO.java b/index-common/src/main/java/com/metamx/druid/index/v1/IndexIO.java
index 5a2c7307ddd..d26e73f5b3c 100644
--- a/index-common/src/main/java/com/metamx/druid/index/v1/IndexIO.java
+++ b/index-common/src/main/java/com/metamx/druid/index/v1/IndexIO.java
@@ -21,6 +21,7 @@ package com.metamx.druid.index.v1;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.base.Preconditions;
+import com.google.common.base.Predicate;
 import com.google.common.collect.ImmutableMap;
 import com.google.common.collect.Iterables;
 import com.google.common.collect.Lists;
@@ -62,7 +63,6 @@ import com.metamx.druid.kv.VSizeIndexedInts;
 import com.metamx.druid.utils.SerializerUtils;
 import it.uniroma3.mat.extendedset.intset.ConciseSet;
 import it.uniroma3.mat.extendedset.intset.ImmutableConciseSet;
-
 import org.joda.time.Interval;
 
 import java.io.ByteArrayOutputStream;
@@ -369,8 +369,8 @@ public class IndexIO
         );
       }
 
-      LinkedHashSet<String> skippedFiles = Sets.newLinkedHashSet();
-      Set<String> skippedDimensions = Sets.newLinkedHashSet();
+      final LinkedHashSet<String> skippedFiles = Sets.newLinkedHashSet();
+      final Set<String> skippedDimensions = Sets.newLinkedHashSet();
       for (String filename : v8SmooshedFiles.getInternalFilenames()) {
         log.info("Processing file[%s]", filename);
         if (filename.startsWith("dim_")) {
@@ -570,25 +570,37 @@ public class IndexIO
       final ByteBuffer indexBuffer = v8SmooshedFiles.mapFile("index.drd");
 
       indexBuffer.get(); // Skip the version byte
-      final GenericIndexed<String> dims = GenericIndexed.read(
+      final GenericIndexed<String> dims8 = GenericIndexed.read(
           indexBuffer, GenericIndexed.stringStrategy
       );
+      final GenericIndexed<String> dims9 = GenericIndexed.fromIterable(
+          Iterables.filter(
+              dims8, new Predicate<String>()
+          {
+            @Override
+            public boolean apply(String s)
+            {
+              return !skippedDimensions.contains(s);
+            }
+          }
+          ),
+          GenericIndexed.stringStrategy
+      );
       final GenericIndexed<String> availableMetrics = GenericIndexed.read(
           indexBuffer, GenericIndexed.stringStrategy
       );
       final Interval dataInterval = new Interval(serializerUtils.readString(indexBuffer));
 
       Set<String> columns = Sets.newTreeSet();
-      columns.addAll(Lists.newArrayList(dims));
+      columns.addAll(Lists.newArrayList(dims9));
       columns.addAll(Lists.newArrayList(availableMetrics));
-      columns.removeAll(skippedDimensions);
 
       GenericIndexed<String> cols = GenericIndexed.fromIterable(columns, GenericIndexed.stringStrategy);
 
-      final int numBytes = cols.getSerializedSize() + dims.getSerializedSize() + 16;
+      final int numBytes = cols.getSerializedSize() + dims9.getSerializedSize() + 16;
       final SmooshedWriter writer = v9Smoosher.addWithSmooshedWriter("index.drd", numBytes);
       cols.writeToChannel(writer);
-      dims.writeToChannel(writer);
+      dims9.writeToChannel(writer);
       serializerUtils.writeLong(writer, dataInterval.getStartMillis());
       serializerUtils.writeLong(writer, dataInterval.getEndMillis());
       writer.close();
diff --git a/server/src/test/java/com/metamx/druid/index/v1/IndexMergerTest.java b/server/src/test/java/com/metamx/druid/index/v1/IndexMergerTest.java
index 86d03f6dd76..407cd36253f 100644
--- a/server/src/test/java/com/metamx/druid/index/v1/IndexMergerTest.java
+++ b/server/src/test/java/com/metamx/druid/index/v1/IndexMergerTest.java
@@ -33,6 +33,7 @@ import org.junit.Test;
 
 import java.io.File;
 import java.util.Arrays;
+import java.util.List;
 
 /**
  */
@@ -116,11 +117,14 @@ public class IndexMergerTest
   @Test
   public void testPersistEmptyColumn() throws Exception
   {
-    final IncrementalIndex toPersist = new IncrementalIndex(0L, QueryGranularity.NONE, new AggregatorFactory[]{});
-    final File tmpDir = Files.createTempDir();
+    final IncrementalIndex toPersist1 = new IncrementalIndex(0L, QueryGranularity.NONE, new AggregatorFactory[]{});
+    final IncrementalIndex toPersist2 = new IncrementalIndex(0L, QueryGranularity.NONE, new AggregatorFactory[]{});
+    final File tmpDir1 = Files.createTempDir();
+    final File tmpDir2 = Files.createTempDir();
+    final File tmpDir3 = Files.createTempDir();
 
     try {
-      toPersist.add(
+      toPersist1.add(
           new MapBasedInputRow(
               1L,
               ImmutableList.of("dim1", "dim2"),
@@ -128,17 +132,32 @@ public class IndexMergerTest
           )
       );
 
-      final QueryableIndex merged = IndexIO.loadIndex(
-          IndexMerger.persist(toPersist, tmpDir)
+      toPersist2.add(
+          new MapBasedInputRow(
+              1L,
+              ImmutableList.of("dim1", "dim2"),
+              ImmutableMap.<String, Object>of("dim1", ImmutableList.of(), "dim2", "bar")
+          )
       );
 
+      final QueryableIndex index1 = IndexIO.loadIndex(IndexMerger.persist(toPersist1, tmpDir1));
+      final QueryableIndex index2 = IndexIO.loadIndex(IndexMerger.persist(toPersist1, tmpDir2));
+      final QueryableIndex merged = IndexIO.loadIndex(
+          IndexMerger.mergeQueryableIndex(Arrays.asList(index1, index2), new AggregatorFactory[]{}, tmpDir3)
+      );
+
+      Assert.assertEquals(1, index1.getTimeColumn().getLength());
+      Assert.assertEquals(ImmutableList.of("dim2"), ImmutableList.copyOf(index1.getAvailableDimensions()));
+
+      Assert.assertEquals(1, index2.getTimeColumn().getLength());
+      Assert.assertEquals(ImmutableList.of("dim2"), ImmutableList.copyOf(index2.getAvailableDimensions()));
+
       Assert.assertEquals(1, merged.getTimeColumn().getLength());
-      Assert.assertEquals(ImmutableList.of("dim1", "dim2"), ImmutableList.copyOf(merged.getAvailableDimensions()));
-      Assert.assertEquals(null, merged.getColumn("dim1"));
+      Assert.assertEquals(ImmutableList.of("dim2"), ImmutableList.copyOf(merged.getAvailableDimensions()));
     } finally {
-      FileUtils.deleteQuietly(tmpDir);
+      FileUtils.deleteQuietly(tmpDir1);
+      FileUtils.deleteQuietly(tmpDir2);
+      FileUtils.deleteQuietly(tmpDir3);
     }
-
-
   }
 }