diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/IndexDiffFilterTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/IndexDiffFilterTest.java
index c95274f68..bb4b066bf 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/IndexDiffFilterTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/IndexDiffFilterTest.java
@@ -134,6 +134,31 @@ public void testFileCommitted() throws Exception {
 		assertFalse(treeWalk.next());
 	}
 
+	@Test
+	public void testConflicts() throws Exception {
+		RevCommit initial = git.commit().setMessage("initial").call();
+		writeTrashFile(FILE, "master");
+		git.add().addFilepattern(FILE).call();
+		RevCommit master = git.commit().setMessage("master").call();
+		git.checkout().setName("refs/heads/side")
+				.setCreateBranch(true).setStartPoint(initial).call();
+		writeTrashFile(FILE, "side");
+		git.add().addFilepattern(FILE).call();
+		RevCommit side = git.commit().setMessage("side").call();
+		assertFalse(git.merge().include("master", master).call()
+				.getMergeStatus()
+				.isSuccessful());
+		assertEquals(read(FILE),
+				"<<<<<<< HEAD\nside\n=======\nmaster\n>>>>>>> master\n");
+		writeTrashFile(FILE, "master");
+
+		TreeWalk treeWalk = createTreeWalk(side);
+		int count = 0;
+		while (treeWalk.next())
+			count++;
+		assertEquals(2, count);
+	}
+
 	@Test
 	public void testFileInFolderCommitted() throws Exception {
 		RevCommit commit = writeFileInFolderAndCommit();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/IndexDiffFilter.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/IndexDiffFilter.java
index 79cd2193f..5aab24caf 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/IndexDiffFilter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/IndexDiffFilter.java
@@ -139,9 +139,13 @@ public boolean include(TreeWalk tw) throws MissingObjectException,
 		DirCacheIterator di = tw.getTree(dirCache, DirCacheIterator.class);
 		if (di != null) {
 			DirCacheEntry dce = di.getDirCacheEntry();
-			if (dce != null)
+			if (dce != null) {
 				if (dce.isAssumeValid())
 					return false;
+				// Never filter index entries with a stage different from 0
+				if (dce.getStage() != 0)
+					return true;
+			}
 		}
 
 		if (!tw.isPostOrderTraversal()) {