diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java
index 383ff5011..251938fec 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java
@@ -56,11 +56,15 @@ import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
 
+import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.api.Status;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEditor;
 import org.eclipse.jgit.dircache.DirCacheEditor.PathEdit;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.errors.ConfigInvalidException;
+import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.lib.Config;
@@ -98,7 +102,7 @@ public class SubmoduleWalkTest extends RepositoryTestCase {
 
 	@Test
 	public void repositoryWithRootLevelSubmodule() throws IOException,
-			ConfigInvalidException {
+			ConfigInvalidException, NoWorkTreeException, GitAPIException {
 		final ObjectId id = ObjectId
 				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
 		final String path = "sub";
@@ -124,6 +128,8 @@ public class SubmoduleWalkTest extends RepositoryTestCase {
 		assertNull(gen.getModulesUpdate());
 		assertNull(gen.getModulesUrl());
 		assertNull(gen.getRepository());
+		Status status = Git.wrap(db).status().call();
+		assertTrue(!status.isClean());
 		assertFalse(gen.next());
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
index 8e0c03ca5..d62b1f58a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
@@ -532,27 +532,29 @@ public class IndexDiff {
 					throw e1;
 				}
 				Repository subRepo = smw.getRepository();
-				ObjectId subHead = subRepo.resolve("HEAD"); //$NON-NLS-1$
-				if (subHead != null && !subHead.equals(smw.getObjectId()))
-					modified.add(smw.getPath());
-				else if (ignoreSubmoduleMode != IgnoreSubmoduleMode.DIRTY) {
-					IndexDiff smid = submoduleIndexDiffs.get(smw.getPath());
-					if (smid == null) {
-						smid = new IndexDiff(subRepo, smw.getObjectId(),
-								wTreeIt.getWorkingTreeIterator(subRepo));
-						submoduleIndexDiffs.put(smw.getPath(), smid);
-					}
-					if (smid.diff()) {
-						if (ignoreSubmoduleMode == IgnoreSubmoduleMode.UNTRACKED
-								&& smid.getAdded().isEmpty()
-								&& smid.getChanged().isEmpty()
-								&& smid.getConflicting().isEmpty()
-								&& smid.getMissing().isEmpty()
-								&& smid.getModified().isEmpty()
-								&& smid.getRemoved().isEmpty()) {
-							continue;
-						}
+				if (subRepo != null) {
+					ObjectId subHead = subRepo.resolve("HEAD"); //$NON-NLS-1$
+					if (subHead != null && !subHead.equals(smw.getObjectId()))
 						modified.add(smw.getPath());
+					else if (ignoreSubmoduleMode != IgnoreSubmoduleMode.DIRTY) {
+						IndexDiff smid = submoduleIndexDiffs.get(smw.getPath());
+						if (smid == null) {
+							smid = new IndexDiff(subRepo, smw.getObjectId(),
+									wTreeIt.getWorkingTreeIterator(subRepo));
+							submoduleIndexDiffs.put(smw.getPath(), smid);
+						}
+						if (smid.diff()) {
+							if (ignoreSubmoduleMode == IgnoreSubmoduleMode.UNTRACKED
+									&& smid.getAdded().isEmpty()
+									&& smid.getChanged().isEmpty()
+									&& smid.getConflicting().isEmpty()
+									&& smid.getMissing().isEmpty()
+									&& smid.getModified().isEmpty()
+									&& smid.getRemoved().isEmpty()) {
+								continue;
+							}
+							modified.add(smw.getPath());
+						}
 					}
 				}
 			}