diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RebaseCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RebaseCommandTest.java
index d574e45f6..7f820b043 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RebaseCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RebaseCommandTest.java
@@ -76,6 +76,10 @@ public class RebaseCommandTest extends RepositoryTestCase {
 
 	private static final String FILE1 = "file1";
 
+	private static final String FILE2 = "file2";
+
+	private static final String FILE3 = "file3";
+
 	protected Git git;
 
 	@Override
@@ -190,6 +194,143 @@ public void testFastForwardWithMultipleCommits() throws Exception {
 				topicLog.get(0).getComment());
 	}
 
+	/**
+	 * Rebase a single root commit onto an independent branch.
+	 *
+	 * <pre>
+	 * A (master)
+	 *
+	 * B - C (orphan)
+	 * </pre>
+	 *
+	 * to
+	 *
+	 * <pre>
+	 * A
+	 *
+	 * B - C (orphan) - A' (master)
+	 * </pre>
+	 *
+	 * @throws Exception
+	 */
+	@Test
+	public void testRebaseRootCommit() throws Exception {
+		writeTrashFile(FILE1, FILE1);
+		writeTrashFile(FILE2, FILE2);
+		git.add().addFilepattern(FILE1).addFilepattern(FILE2).call();
+		RevCommit first = git.commit().setMessage("Add files").call();
+		File file1 = new File(db.getWorkTree(), FILE1);
+		File file2 = new File(db.getWorkTree(), FILE2);
+		assertTrue(file1.exists());
+		assertTrue(file2.exists());
+		// Create an independent branch
+		git.checkout().setOrphan(true).setName("orphan").call();
+		git.rm().addFilepattern(FILE1).addFilepattern(FILE2).call();
+		assertFalse(file1.exists());
+		assertFalse(file2.exists());
+		writeTrashFile(FILE1, "something else");
+		git.add().addFilepattern(FILE1).call();
+		RevCommit orphanBase = git.commit().setMessage("Orphan base").call();
+		writeTrashFile(FILE1, FILE1);
+		git.add().addFilepattern(FILE1).call();
+		RevCommit orphanTop = git.commit().setMessage("Same file1").call();
+		checkoutBranch("refs/heads/master");
+		assertEquals(first.getId(), db.resolve("HEAD"));
+		RebaseResult res = git.rebase().setUpstream("refs/heads/orphan").call();
+		assertEquals(Status.OK, res.getStatus());
+		Iterable<RevCommit> log = git.log().add(db.resolve("HEAD")).call();
+		ObjectId[] ids = { orphanTop.getId(), orphanBase.getId() };
+		int nOfCommits = 0;
+		for (RevCommit c : log) {
+			nOfCommits++;
+			if (nOfCommits == 1) {
+				assertEquals("Add files", c.getFullMessage());
+			} else {
+				assertEquals(ids[nOfCommits - 2], c.getId());
+			}
+		}
+		assertEquals(3, nOfCommits);
+		assertTrue(file1.exists());
+		checkFile(file1, FILE1);
+		assertTrue(file2.exists());
+		checkFile(file2, FILE2);
+	}
+
+	/**
+	 * Rebase a branch onto an independent branch.
+	 *
+	 * <pre>
+	 * A - B (master)
+	 *
+	 * C - D (orphan)
+	 * </pre>
+	 *
+	 * to
+	 *
+	 * <pre>
+	 * A - B
+	 *
+	 * C - D (orphan) - A' - B' (master)
+	 * </pre>
+	 *
+	 * @throws Exception
+	 */
+	@Test
+	public void testRebaseNoMergeBase() throws Exception {
+		writeTrashFile(FILE1, FILE1);
+		writeTrashFile(FILE2, FILE2);
+		git.add().addFilepattern(FILE1).addFilepattern(FILE2).call();
+		git.commit().setMessage("Add files").call();
+		writeTrashFile(FILE3, FILE3);
+		git.add().addFilepattern(FILE3).call();
+		RevCommit first = git.commit().setMessage("File3").call();
+		File file1 = new File(db.getWorkTree(), FILE1);
+		File file2 = new File(db.getWorkTree(), FILE2);
+		File file3 = new File(db.getWorkTree(), FILE3);
+		assertTrue(file1.exists());
+		assertTrue(file2.exists());
+		assertTrue(file3.exists());
+		// Create an independent branch
+		git.checkout().setOrphan(true).setName("orphan").call();
+		git.rm()
+				.addFilepattern(FILE1)
+				.addFilepattern(FILE2)
+				.addFilepattern(FILE3)
+				.call();
+		assertFalse(file1.exists());
+		assertFalse(file2.exists());
+		assertFalse(file3.exists());
+		writeTrashFile(FILE1, "something else");
+		git.add().addFilepattern(FILE1).call();
+		RevCommit orphanBase = git.commit().setMessage("Orphan base").call();
+		writeTrashFile(FILE1, FILE1);
+		git.add().addFilepattern(FILE1).call();
+		RevCommit orphanTop = git.commit().setMessage("Same file1").call();
+		checkoutBranch("refs/heads/master");
+		assertEquals(first.getId(), db.resolve("HEAD"));
+		RebaseResult res = git.rebase().setUpstream("refs/heads/orphan").call();
+		assertEquals(Status.OK, res.getStatus());
+		Iterable<RevCommit> log = git.log().add(db.resolve("HEAD")).call();
+		String[] msgs = { "File3", "Add files" };
+		ObjectId[] ids = { orphanTop.getId(), orphanBase.getId() };
+		int nOfCommits = 0;
+		for (RevCommit c : log) {
+			nOfCommits++;
+			if (nOfCommits <= msgs.length) {
+				assertEquals(msgs[nOfCommits - 1], c.getFullMessage());
+			} else {
+				assertEquals(ids[nOfCommits - msgs.length - 1], c.getId());
+			}
+		}
+		assertEquals(4, nOfCommits);
+		assertTrue(file1.exists());
+		checkFile(file1, FILE1);
+		assertTrue(file2.exists());
+		checkFile(file2, FILE2);
+		assertTrue(file3.exists());
+		checkFile(file3, FILE3);
+	}
+
 	/**
 	 * Create the following commits and then attempt to rebase topic onto
 	 * master. This will serialize the branches.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
index 1e5523f27..19fd3bb2c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
@@ -1217,7 +1217,7 @@ private List<RevCommit> calculatePickList(RevCommit headCommit)
 			Iterator<RevCommit> commitsToUse = r.iterator();
 			while (commitsToUse.hasNext()) {
 				RevCommit commit = commitsToUse.next();
-				if (preserveMerges || commit.getParentCount() == 1) {
+				if (preserveMerges || commit.getParentCount() <= 1) {
 					cherryPickList.add(commit);
 				}
 			}
@@ -1234,23 +1234,31 @@ private List<RevCommit> calculatePickList(RevCommit headCommit)
 			walk.markStart(upstreamCommit);
 			walk.markStart(headCommit);
 			RevCommit base;
-			while ((base = walk.next()) != null)
+			while ((base = walk.next()) != null) {
 				RebaseState.createFile(rewrittenDir, base.getName(),
 						upstreamCommit.getName());
-
+			}
 			Iterator<RevCommit> iterator = cherryPickList.iterator();
 			pickLoop: while(iterator.hasNext()){
 				RevCommit commit = iterator.next();
-				for (int i = 0; i < commit.getParentCount(); i++) {
-					boolean parentRewritten = new File(rewrittenDir, commit
-							.getParent(i).getName()).exists();
-					if (parentRewritten) {
-						new File(rewrittenDir, commit.getName()).createNewFile();
-						continue pickLoop;
+				int nOfParents = commit.getParentCount();
+				if (nOfParents == 0) {
+					// Must be the very first commit in the cherryPickList. We
+					// have independent branches.
+					new File(rewrittenDir, commit.getName()).createNewFile();
+				} else {
+					for (int i = 0; i < nOfParents; i++) {
+						boolean parentRewritten = new File(rewrittenDir,
+								commit.getParent(i).getName()).exists();
+						if (parentRewritten) {
+							new File(rewrittenDir, commit.getName())
+									.createNewFile();
+							continue pickLoop;
+						}
 					}
+					// commit is only merged in, needs not be rewritten
+					iterator.remove();
 				}
-				// commit is only merged in, needs not be rewritten
-				iterator.remove();
 			}
 		}
 		return cherryPickList;