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 6c6292558..a1cec2d91 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
@@ -173,4 +173,39 @@ public class RepositoryCacheTest extends RepositoryTestCase {
 		assertEquals(0, RepositoryCache.getRegisteredKeys().size());
 	}
 
+	@Test
+	public void testRepositoryUsageCount() throws Exception {
+		FileKey loc = FileKey.exact(db.getDirectory(), db.getFS());
+		Repository d2 = RepositoryCache.open(loc);
+		assertEquals(1, d2.useCnt.get());
+		RepositoryCache.open(FileKey.exact(loc.getFile(), db.getFS()));
+		assertEquals(2, d2.useCnt.get());
+		d2.close();
+		assertEquals(1, d2.useCnt.get());
+		d2.close();
+		assertEquals(0, d2.useCnt.get());
+	}
+
+	@Test
+	public void testRepositoryUsageCountWithRegisteredRepository() {
+		assertEquals(1, ((Repository) db).useCnt.get());
+		RepositoryCache.register(db);
+		assertEquals(1, ((Repository) db).useCnt.get());
+		db.close();
+		assertEquals(0, ((Repository) db).useCnt.get());
+	}
+
+	public void testRepositoryUnregisteringWhenClosing() throws Exception {
+		FileKey loc = FileKey.exact(db.getDirectory(), db.getFS());
+		Repository d2 = RepositoryCache.open(loc);
+		assertEquals(1, d2.useCnt.get());
+		assertThat(RepositoryCache.getRegisteredKeys(),
+				hasItem(FileKey.exact(db.getDirectory(), db.getFS())));
+		assertEquals(1, RepositoryCache.getRegisteredKeys().size());
+
+		d2.close();
+
+		assertEquals(0, d2.useCnt.get());
+		assertEquals(0, RepositoryCache.getRegisteredKeys().size());
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
index b8c2fb4a5..6f3166a68 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
@@ -203,10 +203,10 @@ public class RefDirectory extends RefDatabase {
 
 	@Override
 	public void close() {
-		// We have no resources to close.
+		clearReferences();
 	}
 
-	void rescan() {
+	private void clearReferences() {
 		looseRefs.set(RefList.<LooseRef> emptyList());
 		packedRefs.set(PackedRefList.NO_PACKED_REFS);
 	}
@@ -214,7 +214,7 @@ public class RefDirectory extends RefDatabase {
 	@Override
 	public void refresh() {
 		super.refresh();
-		rescan();
+		clearReferences();
 	}
 
 	@Override
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
index f8266133a..ba0dea39f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
@@ -110,7 +110,8 @@ public abstract class Repository implements AutoCloseable {
 		return globalListeners;
 	}
 
-	private final AtomicInteger useCnt = new AtomicInteger(1);
+	/** Use counter */
+	final AtomicInteger useCnt = new AtomicInteger(1);
 
 	/** Metadata directory holding the repository's critical files. */
 	private final File gitDir;
@@ -864,6 +865,7 @@ public abstract class Repository implements AutoCloseable {
 	public void close() {
 		if (useCnt.decrementAndGet() == 0) {
 			doClose();
+			RepositoryCache.unregister(this);
 		}
 	}
 
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 23cc264c1..22b5fcd11 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java
@@ -130,10 +130,10 @@ public class RepositoryCache {
 	}
 
 	/**
-	 * Remove a repository from the cache.
+	 * Close and remove a repository from the cache.
 	 * <p>
-	 * Removes a repository from the cache, if it is still registered here,
-	 * permitting it to close.
+	 * Removes a repository from the cache, if it is still registered here, and
+	 * close it.
 	 *
 	 * @param db
 	 *            repository to unregister.
@@ -141,15 +141,35 @@ public class RepositoryCache {
 	public static void close(final Repository db) {
 		if (db.getDirectory() != null) {
 			FileKey key = FileKey.exact(db.getDirectory(), db.getFS());
-			cache.unregisterRepository(key);
+			cache.unregisterAndCloseRepository(key);
 		}
 	}
 
 	/**
 	 * Remove a repository from the cache.
 	 * <p>
-	 * Removes a repository from the cache, if it is still registered here,
-	 * permitting it to close.
+	 * Removes a repository from the cache, if it is still registered here. This
+	 * method will not close the repository, only remove it from the cache. See
+	 * {@link RepositoryCache#close(Repository)} to remove and close the
+	 * repository.
+	 *
+	 * @param db
+	 *            repository to unregister.
+	 * @since 4.3
+	 */
+	public static void unregister(final Repository db) {
+		if (db.getDirectory() != null) {
+			unregister(FileKey.exact(db.getDirectory(), db.getFS()));
+		}
+	}
+
+	/**
+	 * Remove a repository from the cache.
+	 * <p>
+	 * Removes a repository from the cache, if it is still registered here. This
+	 * method will not close the repository, only remove it from the cache. See
+	 * {@link RepositoryCache#close(Repository)} to remove and close the
+	 * repository.
 	 *
 	 * @param location
 	 *            location of the repository to remove.
@@ -196,15 +216,17 @@ public class RepositoryCache {
 					db = location.open(mustExist);
 					ref = new SoftReference<Repository>(db);
 					cacheMap.put(location, ref);
+				} else {
+					db.incrementOpen();
 				}
 			}
+		} else {
+			db.incrementOpen();
 		}
-		db.incrementOpen();
 		return db;
 	}
 
 	private void registerRepository(final Key location, final Repository db) {
-		db.incrementOpen();
 		SoftReference<Repository> newRef = new SoftReference<Repository>(db);
 		Reference<Repository> oldRef = cacheMap.put(location, newRef);
 		Repository oldDb = oldRef != null ? oldRef.get() : null;
@@ -212,11 +234,16 @@ public class RepositoryCache {
 			oldDb.close();
 	}
 
-	private void unregisterRepository(final Key location) {
+	private Repository unregisterRepository(final Key location) {
 		Reference<Repository> oldRef = cacheMap.remove(location);
-		Repository oldDb = oldRef != null ? oldRef.get() : null;
-		if (oldDb != null)
+		return oldRef != null ? oldRef.get() : null;
+	}
+
+	private void unregisterAndCloseRepository(final Key location) {
+		Repository oldDb = unregisterRepository(location);
+		if (oldDb != null) {
 			oldDb.close();
+		}
 	}
 
 	private Collection<Key> getKeys() {