diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java
index ca5205a..a8eb474 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java
@@ -101,6 +101,9 @@ protected void run() throws Exception {
 		if (localName == null) {
 			try {
 				localName = uri.getHumanishName();
+				if (isBare) {
+					localName = localName + Constants.DOT_GIT_EXT;
+				}
 				localNameF = new File(SystemReader.getInstance().getProperty(
 						Constants.OS_USER_DIR), localName);
 			} catch (IllegalArgumentException e) {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
index ae0b8dd..6ff3b25 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
@@ -76,6 +76,7 @@
 import org.eclipse.jgit.submodule.SubmoduleWalk;
 import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.transport.RemoteConfig;
+import org.eclipse.jgit.transport.URIish;
 import org.eclipse.jgit.util.SystemReader;
 import org.junit.Test;
 
@@ -145,16 +146,36 @@ public void testCloneRepositoryExplicitGitDir() throws IOException,
 		File directory = createTempDirectory("testCloneRepository");
 		CloneCommand command = Git.cloneRepository();
 		command.setDirectory(directory);
-		command.setGitDir(new File(directory, ".git"));
+		command.setGitDir(new File(directory, Constants.DOT_GIT));
 		command.setURI(fileUri());
 		Git git2 = command.call();
 		addRepoToClose(git2.getRepository());
 		assertEquals(directory, git2.getRepository().getWorkTree());
-		assertEquals(new File(directory, ".git"), git2.getRepository()
+		assertEquals(new File(directory, Constants.DOT_GIT), git2.getRepository()
 				.getDirectory());
 	}
 
 	@Test
+	public void testCloneRepositoryDefaultDirectory() throws IOException, URISyntaxException,
+			JGitInternalException, GitAPIException {
+		CloneCommand command = Git.cloneRepository().setURI(fileUri());
+
+		command.verifyDirectories(new URIish(fileUri()));
+		File directory = command.getDirectory();
+		assertEquals(git.getRepository().getWorkTree().getName(), directory.getName());
+	}
+
+	@Test
+	public void testCloneBareRepositoryDefaultDirectory() throws IOException, URISyntaxException,
+			JGitInternalException, GitAPIException {
+		CloneCommand command = Git.cloneRepository().setURI(fileUri()).setBare(true);
+
+		command.verifyDirectories(new URIish(fileUri()));
+		File directory = command.getDirectory();
+		assertEquals(git.getRepository().getWorkTree().getName() + Constants.DOT_GIT_EXT, directory.getName());
+	}
+
+	@Test
 	public void testCloneRepositoryExplicitGitDirNonStd() throws IOException,
 			JGitInternalException, GitAPIException {
 		File directory = createTempDirectory("testCloneRepository");
@@ -168,8 +189,8 @@ public void testCloneRepositoryExplicitGitDirNonStd() throws IOException,
 		assertEquals(directory, git2.getRepository().getWorkTree());
 		assertEquals(gDir, git2.getRepository()
 				.getDirectory());
-		assertTrue(new File(directory, ".git").isFile());
-		assertFalse(new File(gDir, ".git").exists());
+		assertTrue(new File(directory, Constants.DOT_GIT).isFile());
+		assertFalse(new File(gDir, Constants.DOT_GIT).exists());
 	}
 
 	@Test
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
index d450c64..bde8e63 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
@@ -50,6 +50,7 @@
 import java.util.Collection;
 import java.util.List;
 
+import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRemoteException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
@@ -157,6 +158,16 @@ public CloneCommand() {
 	}
 
 	/**
+	 * Get the git directory. This is primarily used for tests.
+	 *
+	 * @return the git directory
+	 */
+	@Nullable
+	File getDirectory() {
+		return directory;
+	}
+
+	/**
 	 * Executes the {@code Clone} command.
 	 *
 	 * The Git instance returned by this command needs to be closed by the
@@ -232,9 +243,9 @@ private static boolean isNonEmptyDirectory(File dir) {
 		return false;
 	}
 
-	private void verifyDirectories(URIish u) {
+	void verifyDirectories(URIish u) {
 		if (directory == null && gitDir == null) {
-			directory = new File(u.getHumanishName(), Constants.DOT_GIT);
+			directory = new File(u.getHumanishName() + (bare ? Constants.DOT_GIT_EXT : "")); //$NON-NLS-1$
 		}
 		directoryExistsInitially = directory != null && directory.exists();
 		gitDirExistsInitially = gitDir != null && gitDir.exists();