diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RepositoryCacheTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RepositoryCacheTest.java
index 6bea32012..b44b4c34a 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RepositoryCacheTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RepositoryCacheTest.java
@@ -209,6 +209,27 @@ public class RepositoryCacheTest extends RepositoryTestCase {
 		assertTrue(RepositoryCache.isCached(d2));
 	}
 
+	@Test
+	public void testRepositoryUnregisteringWhenExpiredAndUsageCountNegative()
+			throws Exception {
+		Repository repoA = createBareRepository();
+		RepositoryCache.register(repoA);
+
+		assertEquals(1, RepositoryCache.getRegisteredKeys().size());
+		assertTrue(RepositoryCache.isCached(repoA));
+
+		// close the repo twice to make usage count negative
+		repoA.close();
+		repoA.close();
+		// fake that repoA was closed more than 1 hour ago (default expiration
+		// time)
+		repoA.closedAt.set(System.currentTimeMillis() - 65 * 60 * 1000);
+
+		RepositoryCache.clearExpired();
+
+		assertEquals(0, RepositoryCache.getRegisteredKeys().size());
+	}
+
 	@Test
 	public void testRepositoryUnregisteringWhenExpired() throws Exception {
 		Repository repoA = createBareRepository();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java
index e5a0553ab..9a57349f5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java
@@ -298,7 +298,7 @@ public class RepositoryCache {
 	}
 
 	private boolean isExpired(Repository db) {
-		return db != null && db.useCnt.get() == 0
+		return db != null && db.useCnt.get() <= 0
 			&& (System.currentTimeMillis() - db.closedAt.get() > expireAfter);
 	}
 
@@ -325,15 +325,9 @@ public class RepositoryCache {
 	}
 
 	private void clearAll() {
-		for (int stage = 0; stage < 2; stage++) {
-			for (Iterator<Map.Entry<Key, Reference<Repository>>> i = cacheMap
-					.entrySet().iterator(); i.hasNext();) {
-				final Map.Entry<Key, Reference<Repository>> e = i.next();
-				final Repository db = e.getValue().get();
-				if (db != null)
-					db.close();
-				i.remove();
-			}
+		for (Iterator<Map.Entry<Key, Reference<Repository>>> i = cacheMap
+				.entrySet().iterator(); i.hasNext();) {
+			unregisterAndCloseRepository(i.next().getKey());
 		}
 	}