diff --git a/hbase-server/src/main/java/org/apache/hadoop/hbase/master/CatalogJanitor.java b/hbase-server/src/main/java/org/apache/hadoop/hbase/master/CatalogJanitor.java
index e751f65a8b4..1492548c22c 100644
--- a/hbase-server/src/main/java/org/apache/hadoop/hbase/master/CatalogJanitor.java
+++ b/hbase-server/src/main/java/org/apache/hadoop/hbase/master/CatalogJanitor.java
@@ -22,6 +22,7 @@ package org.apache.hadoop.hbase.master;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.Comparator;
+import java.util.HashSet;
 import java.util.Map;
 import java.util.TreeMap;
 import java.util.concurrent.atomic.AtomicInteger;
@@ -99,11 +100,10 @@ class CatalogJanitor extends Chore {
   }
 
   /**
-   * Run janitorial scan of catalog <code>.META.</code> table looking for
-   * garbage to collect.
-   * @throws IOException
+   * Scans META and returns a number of scanned rows, and
+   * an ordered map of split parents.
    */
-  void scan() throws IOException {
+  Pair<Integer, Map<HRegionInfo, Result>> getSplitParents() throws IOException {
     // TODO: Only works with single .META. region currently.  Fix.
     final AtomicInteger count = new AtomicInteger(0);
     // Keep Map of found split parents.  There are candidates for cleanup.
@@ -125,18 +125,40 @@ class CatalogJanitor extends Chore {
     };
     // Run full scan of .META. catalog table passing in our custom visitor
     MetaReader.fullScan(this.server.getCatalogTracker(), visitor);
+
+    return new Pair<Integer, Map<HRegionInfo, Result>>(count.get(), splitParents);
+  }
+
+  /**
+   * Run janitorial scan of catalog <code>.META.</code> table looking for
+   * garbage to collect.
+   * @throws IOException
+   */
+  int scan() throws IOException {
+    Pair<Integer, Map<HRegionInfo, Result>> pair = getSplitParents();
+    int count = pair.getFirst();
+    Map<HRegionInfo, Result> splitParents = pair.getSecond();
+
     // Now work on our list of found parents. See if any we can clean up.
     int cleaned = 0;
+    HashSet<HRegionInfo> parentNotCleaned = new HashSet<HRegionInfo>(); //regions whose parents are still around
     for (Map.Entry<HRegionInfo, Result> e : splitParents.entrySet()) {
-      if (cleanParent(e.getKey(), e.getValue())) cleaned++;
+      if (!parentNotCleaned.contains(e.getKey()) && cleanParent(e.getKey(), e.getValue())) {
+        cleaned++;
+      } else {
+        // We could not clean the parent, so it's daughters should not be cleaned either (HBASE-6160)
+        parentNotCleaned.add(getDaughterRegionInfo(e.getValue(), HConstants.SPLITA_QUALIFIER));
+        parentNotCleaned.add(getDaughterRegionInfo(e.getValue(), HConstants.SPLITB_QUALIFIER));
+      }
     }
     if (cleaned != 0) {
-      LOG.info("Scanned " + count.get() + " catalog row(s) and gc'd " + cleaned +
+      LOG.info("Scanned " + count + " catalog row(s) and gc'd " + cleaned +
         " unreferenced parent region(s)");
     } else if (LOG.isDebugEnabled()) {
-      LOG.debug("Scanned " + count.get() + " catalog row(s) and gc'd " + cleaned +
+      LOG.debug("Scanned " + count + " catalog row(s) and gc'd " + cleaned +
       " unreferenced parent region(s)");
     }
+    return cleaned;
   }
 
   /**
diff --git a/hbase-server/src/test/java/org/apache/hadoop/hbase/master/TestCatalogJanitor.java b/hbase-server/src/test/java/org/apache/hadoop/hbase/master/TestCatalogJanitor.java
index 5c16e343515..2495987dd0e 100644
--- a/hbase-server/src/test/java/org/apache/hadoop/hbase/master/TestCatalogJanitor.java
+++ b/hbase-server/src/test/java/org/apache/hadoop/hbase/master/TestCatalogJanitor.java
@@ -23,6 +23,9 @@ import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertEquals;
+import static org.mockito.Mockito.doReturn;
+import static org.mockito.Mockito.spy;
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
@@ -55,11 +58,13 @@ import org.apache.hadoop.hbase.client.HConnectionTestingUtility;
 import org.apache.hadoop.hbase.client.Result;
 import org.apache.hadoop.hbase.executor.ExecutorService;
 import org.apache.hadoop.hbase.io.Reference;
+import org.apache.hadoop.hbase.master.CatalogJanitor.SplitParentFirstComparator;
 import org.apache.hadoop.hbase.protobuf.ProtobufUtil;
 import org.apache.hadoop.hbase.protobuf.generated.ClientProtos.MutateRequest;
 import org.apache.hadoop.hbase.protobuf.generated.ClientProtos.MutateResponse;
 import org.apache.hadoop.hbase.regionserver.Store;
 import org.apache.hadoop.hbase.util.Bytes;
+import org.apache.hadoop.hbase.util.Pair;
 import org.apache.hadoop.hbase.util.Writables;
 import org.apache.hadoop.hbase.zookeeper.ZooKeeperWatcher;
 import org.junit.Test;
@@ -490,6 +495,96 @@ public class TestCatalogJanitor {
     janitor.join();
   }
 
+  /**
+   * CatalogJanitor.scan() should not clean parent regions if their own
+   * parents are still referencing them. This ensures that grandfather regions
+   * do not point to deleted parent regions.
+   */
+  @Test
+  public void testScanDoesNotCleanRegionsWithExistingParents() throws Exception {
+    HBaseTestingUtility htu = new HBaseTestingUtility();
+    setRootDirAndCleanIt(htu, "testScanDoesNotCleanRegionsWithExistingParents");
+    Server server = new MockServer(htu);
+    MasterServices services = new MockMasterServices(server);
+
+    final HTableDescriptor htd = createHTableDescriptor();
+
+    // Create regions: aaa->{lastEndKey}, aaa->ccc, aaa->bbb, bbb->ccc, etc.
+
+    // Parent
+    HRegionInfo parent = new HRegionInfo(htd.getName(), Bytes.toBytes("aaa"),
+      new byte[0], true);
+    // Sleep a second else the encoded name on these regions comes out
+    // same for all with same start key and made in same second.
+    Thread.sleep(1001);
+
+    // Daughter a
+    HRegionInfo splita = new HRegionInfo(htd.getName(), Bytes.toBytes("aaa"),
+      Bytes.toBytes("ccc"), true);
+    Thread.sleep(1001);
+    // Make daughters of daughter a; splitaa and splitab.
+    HRegionInfo splitaa = new HRegionInfo(htd.getName(), Bytes.toBytes("aaa"),
+      Bytes.toBytes("bbb"), false);
+    HRegionInfo splitab = new HRegionInfo(htd.getName(), Bytes.toBytes("bbb"),
+      Bytes.toBytes("ccc"), false);
+
+    // Daughter b
+    HRegionInfo splitb = new HRegionInfo(htd.getName(), Bytes.toBytes("ccc"),
+        new byte[0]);
+    Thread.sleep(1001);
+
+    final Map<HRegionInfo, Result> splitParents =
+        new TreeMap<HRegionInfo, Result>(new SplitParentFirstComparator());
+    splitParents.put(parent, makeResultFromHRegionInfo(parent, splita, splitb));
+    splitParents.put(splita, makeResultFromHRegionInfo(splita, splitaa, splitab));
+
+    CatalogJanitor janitor = spy(new CatalogJanitor(server, services));
+    doReturn(new Pair<Integer, Map<HRegionInfo, Result>>(
+        10, splitParents)).when(janitor).getSplitParents();
+
+    //create ref from splita to parent
+    Path splitaRef =
+        createReferences(services, htd, parent, splita, Bytes.toBytes("ccc"), false);
+
+    //parent and A should not be removed
+    assertEquals(0, janitor.scan());
+
+    //now delete the ref
+    FileSystem fs = FileSystem.get(htu.getConfiguration());
+    assertTrue(fs.delete(splitaRef, true));
+
+    //now, both parent, and splita can be deleted
+    assertEquals(2, janitor.scan());
+
+    services.stop("test finished");
+    janitor.join();
+  }
+
+  private Result makeResultFromHRegionInfo(HRegionInfo region, HRegionInfo splita,
+      HRegionInfo splitb) throws IOException {
+    List<KeyValue> kvs = new ArrayList<KeyValue>();
+    kvs.add(new KeyValue(
+        region.getRegionName(),
+        HConstants.CATALOG_FAMILY, HConstants.REGIONINFO_QUALIFIER,
+        Writables.getBytes(region)));
+
+    if (splita != null) {
+      kvs.add(new KeyValue(
+          region.getRegionName(),
+          HConstants.CATALOG_FAMILY, HConstants.SPLITA_QUALIFIER,
+          Writables.getBytes(splita)));
+    }
+
+    if (splitb != null) {
+      kvs.add(new KeyValue(
+          region.getRegionName(),
+          HConstants.CATALOG_FAMILY, HConstants.SPLITB_QUALIFIER,
+          Writables.getBytes(splitb)));
+    }
+
+    return new Result(kvs);
+  }
+
   private String setRootDirAndCleanIt(final HBaseTestingUtility htu,
       final String subdir)
   throws IOException {