diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PathCheckoutCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PathCheckoutCommandTest.java
index 1ec278753..81b6908dc 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PathCheckoutCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PathCheckoutCommandTest.java
@@ -45,7 +45,12 @@ package org.eclipse.jgit.api;
 import static org.junit.Assert.assertEquals;
 
 import java.io.File;
+import java.io.IOException;
 
+import org.eclipse.jgit.dircache.DirCache;
+import org.eclipse.jgit.dircache.DirCacheEntry;
+import org.eclipse.jgit.errors.NoWorkTreeException;
+import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.RepositoryTestCase;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.junit.Before;
@@ -60,6 +65,8 @@ public class PathCheckoutCommandTest extends RepositoryTestCase {
 
 	private static final String FILE2 = "Test2.txt";
 
+	private static final String FILE3 = "Test3.txt";
+
 	Git git;
 
 	RevCommit initialCommit;
@@ -148,4 +155,49 @@ public class PathCheckoutCommandTest extends RepositoryTestCase {
 		assertEquals("c", read(new File(db.getWorkTree(), FILE2)));
 	}
 
+	@Test
+	public void testUpdateWorkingDirectoryFromIndex2() throws Exception {
+		CheckoutCommand co = git.checkout();
+		fsTick(git.getRepository().getIndexFile());
+
+		File written1 = writeTrashFile(FILE1, "3(modified)");
+		File written2 = writeTrashFile(FILE2, "a(modified)");
+		fsTick(written2);
+
+		// make sure that we get unsmudged entries for FILE1 and FILE2
+		writeTrashFile(FILE3, "foo");
+		git.add().addFilepattern(FILE3).call();
+		fsTick(git.getRepository().getIndexFile());
+
+		git.add().addFilepattern(FILE1).addFilepattern(FILE2).call();
+		fsTick(git.getRepository().getIndexFile());
+
+		writeTrashFile(FILE1, "3(modified again)");
+		writeTrashFile(FILE2, "a(modified again)");
+		fsTick(written2);
+
+		co.addPath(FILE1).setStartPoint(secondCommit).call();
+
+		assertEquals("2", read(written1));
+		assertEquals("a(modified again)", read(written2));
+
+		validateIndex(git);
+	}
+
+	public static void validateIndex(Git git) throws NoWorkTreeException,
+			IOException {
+		DirCache dc = git.getRepository().lockDirCache();
+		ObjectReader r = git.getRepository().getObjectDatabase().newReader();
+		try {
+			for (int i = 0; i < dc.getEntryCount(); ++i) {
+				DirCacheEntry entry = dc.getEntry(i);
+				if (entry.getLength() > 0)
+					assertEquals(entry.getLength(), r.getObjectSize(
+							entry.getObjectId(), ObjectReader.OBJ_ANY));
+			}
+		} finally {
+			dc.unlock();
+			r.release();
+		}
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
index dd9f0c456..6f2570a40 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
@@ -65,6 +65,7 @@ import org.eclipse.jgit.errors.AmbiguousObjectException;
 import org.eclipse.jgit.errors.CheckoutConflictException;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.Ref;
@@ -245,40 +246,42 @@ public class CheckoutCommand extends GitCommand<Ref> {
 		RevWalk revWalk = new RevWalk(repo);
 		DirCache dc = repo.lockDirCache();
 		try {
-			TreeWalk treeWalk = new TreeWalk(revWalk.getObjectReader());
-			treeWalk.setRecursive(true);
-			treeWalk.addTree(new DirCacheIterator(dc));
-			treeWalk.setFilter(PathFilterGroup.createFromStrings(paths));
-			List<String> files = new LinkedList<String>();
-			while (treeWalk.next())
-				files.add(treeWalk.getPathString());
-
-			if (startCommit != null || startPoint != null) {
-				DirCacheEditor editor = dc.editor();
-				TreeWalk startWalk = new TreeWalk(revWalk.getObjectReader());
-				startWalk.setRecursive(true);
-				startWalk.setFilter(treeWalk.getFilter());
+			DirCacheEditor editor = dc.editor();
+			TreeWalk startWalk = new TreeWalk(revWalk.getObjectReader());
+			startWalk.setRecursive(true);
+			startWalk.setFilter(PathFilterGroup.createFromStrings(paths));
+			boolean checkoutIndex = startCommit == null && startPoint == null;
+			if (!checkoutIndex)
 				startWalk.addTree(revWalk.parseCommit(getStartPoint())
 						.getTree());
+			else
+				startWalk.addTree(new DirCacheIterator(dc));
+
+			final File workTree = repo.getWorkTree();
+			final ObjectReader r = repo.getObjectDatabase().newReader();
+			try {
 				while (startWalk.next()) {
 					final ObjectId blobId = startWalk.getObjectId(0);
+					final FileMode mode = startWalk.getFileMode(0);
 					editor.add(new PathEdit(startWalk.getPathString()) {
-
 						public void apply(DirCacheEntry ent) {
 							ent.setObjectId(blobId);
+							ent.setFileMode(mode);
+							try {
+								DirCacheCheckout.checkoutEntry(repo, new File(
+										workTree, ent.getPathString()), ent, r);
+							} catch (IOException e) {
+								throw new JGitInternalException(
+										MessageFormat.format(
+												JGitText.get().checkoutConflictWithFile,
+												ent.getPathString()), e);
+							}
 						}
 					});
 				}
 				editor.commit();
-			}
-
-			File workTree = repo.getWorkTree();
-			ObjectReader r = repo.getObjectDatabase().newReader();
-			try {
-				for (String file : files)
-					DirCacheCheckout.checkoutEntry(repo, new File(workTree,
-							file), dc.getEntry(file), r);
 			} finally {
+				startWalk.release();
 				r.release();
 			}
 		} finally {