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 59d10f68c..eccaa5514 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
@@ -58,6 +58,7 @@ import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.treewalk.WorkingTreeIterator;
 import org.eclipse.jgit.treewalk.filter.AndTreeFilter;
 import org.eclipse.jgit.treewalk.filter.NotIgnoredFilter;
+import org.eclipse.jgit.treewalk.filter.SkipWorkTreeFilter;
 import org.eclipse.jgit.treewalk.filter.TreeFilter;
 
 /**
@@ -160,8 +161,9 @@ public class IndexDiff {
 		treeWalk.addTree(new DirCacheIterator(dirCache));
 		treeWalk.addTree(initialWorkingTreeIterator);
 		treeWalk.setFilter(TreeFilter.ANY_DIFF);
-		treeWalk.setFilter(AndTreeFilter.create(TreeFilter.ANY_DIFF,
-				new NotIgnoredFilter(WORKDIR)));
+		treeWalk.setFilter(AndTreeFilter.create(new TreeFilter[] {
+				new NotIgnoredFilter(WORKDIR), new SkipWorkTreeFilter(INDEX),
+				TreeFilter.ANY_DIFF }));
 		while (treeWalk.next()) {
 			AbstractTreeIterator treeIterator = treeWalk.getTree(TREE,
 					AbstractTreeIterator.class);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/SkipWorkTreeFilter.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/SkipWorkTreeFilter.java
new file mode 100644
index 000000000..d06a13ed8
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/SkipWorkTreeFilter.java
@@ -0,0 +1,96 @@
+/*
+ * Copyright (C) 2010, Google Inc.
+ * Copyright (C) 2010, Marc Strapetz <marc.strapetz@syntevo.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.treewalk.filter;
+
+import org.eclipse.jgit.dircache.DirCacheEntry;
+import org.eclipse.jgit.dircache.DirCacheIterator;
+import org.eclipse.jgit.treewalk.TreeWalk;
+
+/**
+ * To be used in combination with a DirCacheIterator: includes only tree entries
+ * for which 'skipWorkTree' flag is not set.
+ */
+public class SkipWorkTreeFilter extends TreeFilter {
+
+	/** Index of DirCacheIterator to work on. */
+	private final int treeIdx;
+
+	/**
+	 * Create a filter to work on the specified DirCacheIterator.
+	 *
+	 * @param treeIdx
+	 *            index of DirCacheIterator to work on. If the index does not
+	 *            refer to a DirCacheIterator, the filter will include all
+	 *            entries.
+	 */
+	public SkipWorkTreeFilter(int treeIdx) {
+		this.treeIdx = treeIdx;
+	}
+
+	@Override
+	public boolean include(TreeWalk walker) {
+		DirCacheIterator i = walker.getTree(treeIdx, DirCacheIterator.class);
+		if (i == null)
+			return true;
+
+		DirCacheEntry e = i.getDirCacheEntry();
+		return e == null || !e.isSkipWorkTree();
+	}
+
+	@Override
+	public boolean shouldBeRecursive() {
+		return false;
+	}
+
+	@Override
+	public TreeFilter clone() {
+		return this;
+	}
+
+	@Override
+	public String toString() {
+		return "SkipWorkTree(" + treeIdx + ")";
+	}
+}