diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
index 2fb228e01..07173a9c3 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
@@ -44,7 +44,9 @@
 package org.eclipse.jgit.api;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
 import java.io.File;
@@ -61,6 +63,7 @@ import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectInserter;
+import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryTestCase;
 import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevCommit;
@@ -684,6 +687,40 @@ public class AddCommandTest extends RepositoryTestCase {
 		assertEquals(FileMode.EXECUTABLE_FILE, walk.getFileMode(0));
 	}
 
+	@Test
+	public void testSubmoduleDeleteNotStagedWithUpdate() throws Exception {
+		Git git = new Git(db);
+		writeTrashFile("file.txt", "content");
+		git.add().addFilepattern("file.txt").call();
+		assertNotNull(git.commit().setMessage("create file").call());
+
+		SubmoduleAddCommand command = new SubmoduleAddCommand(db);
+		String path = "sub";
+		command.setPath(path);
+		String uri = db.getDirectory().toURI().toString();
+		command.setURI(uri);
+		Repository repo = command.call();
+		assertNotNull(repo);
+		assertNotNull(git.commit().setMessage("add submodule").call());
+
+		assertTrue(git.status().call().isClean());
+
+		FileUtils.delete(repo.getWorkTree(), FileUtils.RECURSIVE);
+		FileUtils.mkdir(new File(db.getWorkTree(), path), false);
+
+		assertNotNull(git.add().addFilepattern(".").setUpdate(true).call());
+
+		Status status = git.status().call();
+		assertFalse(status.isClean());
+		assertTrue(status.getAdded().isEmpty());
+		assertTrue(status.getChanged().isEmpty());
+		assertTrue(status.getRemoved().isEmpty());
+		assertTrue(status.getUntracked().isEmpty());
+		assertTrue(status.getModified().isEmpty());
+		assertEquals(1, status.getMissing().size());
+		assertEquals(path, status.getMissing().iterator().next());
+	}
+
 	private DirCacheEntry addEntryToBuilder(String path, File file,
 			ObjectInserter newObjectInserter, DirCacheBuilder builder, int stage)
 			throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
index f3e47ae01..867945362 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
@@ -203,9 +203,10 @@ public class AddCommand extends GitCommand<DirCache> {
 								builder.add(c.getDirCacheEntry());
 							}
 
-						} else if (!update){
+						} else if (c != null
+								&& (!update || FileMode.GITLINK == c
+										.getEntryFileMode()))
 							builder.add(c.getDirCacheEntry());
-						}
 					}
 				}
 			}