Index: lucene/core/src/java/org/apache/lucene/index/ParallelCompositeReader.java
===================================================================
--- lucene/core/src/java/org/apache/lucene/index/ParallelCompositeReader.java	(revision 1245583)
+++ lucene/core/src/java/org/apache/lucene/index/ParallelCompositeReader.java	(working copy)
@@ -90,11 +90,13 @@
       // check compatibility:
       final int maxDoc = readers[0].maxDoc();
       final int[] childMaxDoc = new int[firstSubReaders.length];
+      final boolean[] childAtomic = new boolean[firstSubReaders.length];
       for (int i = 0; i < firstSubReaders.length; i++) {
         childMaxDoc[i] = firstSubReaders[i].maxDoc();
+        childAtomic[i] = firstSubReaders[i] instanceof AtomicReader;
       }
-      validate(readers, maxDoc, childMaxDoc);
-      validate(storedFieldsReaders, maxDoc, childMaxDoc);
+      validate(readers, maxDoc, childMaxDoc, childAtomic);
+      validate(storedFieldsReaders, maxDoc, childMaxDoc, childAtomic);
 
       // hierarchically build the same subreader structure as the first CompositeReader with Parallel*Readers:
       final IndexReader[] subReaders = new IndexReader[firstSubReaders.length];
@@ -131,7 +133,7 @@
     }
   }
   
-  private static void validate(CompositeReader[] readers, int maxDoc, int[] childMaxDoc) {
+  private static void validate(CompositeReader[] readers, int maxDoc, int[] childMaxDoc, boolean[] childAtomic) {
     for (int i = 0; i < readers.length; i++) {
       final CompositeReader reader = readers[i];
       final IndexReader[] subs = reader.getSequentialSubReaders();
@@ -143,8 +145,11 @@
       }
       for (int subIDX = 0; subIDX < subs.length; subIDX++) {
         if (subs[subIDX].maxDoc() != childMaxDoc[subIDX]) {
-          throw new IllegalArgumentException("All readers must have same subReader maxDoc");
+          throw new IllegalArgumentException("All readers must have same corresponding subReader maxDoc");
         }
+        if (!(childAtomic[subIDX] ? (subs[subIDX] instanceof AtomicReader) : (subs[subIDX] instanceof CompositeReader))) {
+          throw new IllegalArgumentException("All readers must have same corresponding subReader types (atomic or composite)");
+        }
       }
     }    
   }
Index: lucene/core/src/test/org/apache/lucene/index/TestParallelCompositeReader.java
===================================================================
--- lucene/core/src/test/org/apache/lucene/index/TestParallelCompositeReader.java	(revision 1245583)
+++ lucene/core/src/test/org/apache/lucene/index/TestParallelCompositeReader.java	(working copy)
@@ -34,9 +34,32 @@
   private Directory dir, dir1, dir2;
 
   public void testQueries() throws Exception {
-    single = single(random);
-    parallel = parallel(random);
+    single = single(random, false);
+    parallel = parallel(random, false);
     
+    queries();
+    
+    single.getIndexReader().close(); single = null;
+    parallel.getIndexReader().close(); parallel = null;
+    dir.close(); dir = null;
+    dir1.close(); dir1 = null;
+    dir2.close(); dir2 = null;
+  }
+
+  public void testQueriesCompositeComposite() throws Exception {
+    single = single(random, true);
+    parallel = parallel(random, true);
+    
+    queries();
+    
+    single.getIndexReader().close(); single = null;
+    parallel.getIndexReader().close(); parallel = null;
+    dir.close(); dir = null;
+    dir1.close(); dir1 = null;
+    dir2.close(); dir2 = null;
+  }
+  
+  private void queries() throws Exception {
     queryTest(new TermQuery(new Term("f1", "v1")));
     queryTest(new TermQuery(new Term("f1", "v2")));
     queryTest(new TermQuery(new Term("f2", "v1")));
@@ -50,12 +73,6 @@
     bq1.add(new TermQuery(new Term("f1", "v1")), Occur.MUST);
     bq1.add(new TermQuery(new Term("f4", "v1")), Occur.MUST);
     queryTest(bq1);
-    
-    single.getIndexReader().close(); single = null;
-    parallel.getIndexReader().close(); parallel = null;
-    dir.close(); dir = null;
-    dir1.close(); dir1 = null;
-    dir2.close(); dir2 = null;
   }
 
   public void testRefCounts1() throws IOException {
@@ -142,7 +159,7 @@
         ir2 = DirectoryReader.open(dir2);
     CompositeReader[] readers = new CompositeReader[] {ir1, ir2};
     try {
-      new ParallelCompositeReader(ir1, ir2);
+      new ParallelCompositeReader(readers);
       fail("didn't get expected exception: indexes don't have same subreader structure");
     } catch (IllegalArgumentException e) {
       // expected exception
@@ -163,6 +180,35 @@
     dir2.close();
   }
   
+  public void testIncompatibleIndexes3() throws IOException {
+    Directory dir1 = getDir1(random);
+    Directory dir2 = getDir2(random);
+
+    CompositeReader ir1 = new MultiReader(DirectoryReader.open(dir1), SlowCompositeReaderWrapper.wrap(DirectoryReader.open(dir1))),
+        ir2 = new MultiReader(DirectoryReader.open(dir2), DirectoryReader.open(dir2));
+    CompositeReader[] readers = new CompositeReader[] {ir1, ir2};
+    try {
+      new ParallelCompositeReader(readers);
+      fail("didn't get expected exception: indexes don't have same subreader structure");
+    } catch (IllegalArgumentException e) {
+      // expected exception
+    }
+    try {
+      new ParallelCompositeReader(random.nextBoolean(), readers, readers);
+      fail("didn't get expected exception: indexes don't have same subreader structure");
+    } catch (IllegalArgumentException e) {
+      // expected exception
+    }
+    assertEquals(1, ir1.getRefCount());
+    assertEquals(1, ir2.getRefCount());
+    ir1.close();
+    ir2.close();
+    assertEquals(0, ir1.getRefCount());
+    assertEquals(0, ir2.getRefCount());
+    dir1.close();
+    dir2.close();
+  }
+  
   public void testIgnoreStoredFields() throws IOException {
     Directory dir1 = getDir1(random);
     Directory dir2 = getDir2(random);
@@ -247,7 +293,7 @@
   }
 
   // Fields 1-4 indexed together:
-  private IndexSearcher single(Random random) throws IOException {
+  private IndexSearcher single(Random random, boolean compositeComposite) throws IOException {
     dir = newDirectory();
     IndexWriter w = new IndexWriter(dir, newIndexWriterConfig( TEST_VERSION_CURRENT, new MockAnalyzer(random)));
     Document d1 = new Document();
@@ -276,18 +322,31 @@
     w.addDocument(d4);
     w.close();
 
-    DirectoryReader ir = DirectoryReader.open(dir);
+    final CompositeReader ir;
+    if (compositeComposite) {
+      ir = new MultiReader(DirectoryReader.open(dir), DirectoryReader.open(dir));
+    } else {
+      ir = DirectoryReader.open(dir);
+    }
     return newSearcher(ir);
   }
 
   // Fields 1 & 2 in one index, 3 & 4 in other, with ParallelReader:
-  private IndexSearcher parallel(Random random) throws IOException {
+  private IndexSearcher parallel(Random random, boolean compositeComposite) throws IOException {
     dir1 = getDir1(random);
     dir2 = getDir2(random);
-    final DirectoryReader rd1 = DirectoryReader.open(dir1),
+    final CompositeReader rd1, rd2;
+    if (compositeComposite) {
+      rd1 = new MultiReader(DirectoryReader.open(dir1), DirectoryReader.open(dir1));
+      rd2 = new MultiReader(DirectoryReader.open(dir2), DirectoryReader.open(dir2));
+      assertEquals(2, rd1.getSequentialSubReaders().length);
+      assertEquals(2, rd2.getSequentialSubReaders().length);
+    } else {
+      rd1 = DirectoryReader.open(dir1);
       rd2 = DirectoryReader.open(dir2);
-    assertEquals(3, rd1.getSequentialSubReaders().length);
-    assertEquals(3, rd2.getSequentialSubReaders().length);
+      assertEquals(3, rd1.getSequentialSubReaders().length);
+      assertEquals(3, rd2.getSequentialSubReaders().length);
+    }
     ParallelCompositeReader pr = new ParallelCompositeReader(rd1, rd2);
     return newSearcher(pr);
   }