diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepositoryTestCase.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepositoryTestCase.java
index 1f1962a7b..7b12ce1b2 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepositoryTestCase.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepositoryTestCase.java
@@ -498,4 +498,9 @@ protected DirCacheEntry createEntry(final String path, final FileMode mode,
 				Constants.OBJ_BLOB, Constants.encode(content)));
 		return entry;
 	}
+
+	public static void assertEqualsFile(File expected, File actual)
+			throws IOException {
+		assertEquals(expected.getCanonicalFile(), actual.getCanonicalFile());
+	}
 }
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 aad5bfc83..0cab987e6 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
@@ -61,17 +61,17 @@
 
 public class RepositoryCacheTest extends RepositoryTestCase {
 	@Test
-	public void testNonBareFileKey() {
+	public void testNonBareFileKey() throws IOException {
 		File gitdir = db.getDirectory();
 		File parent = gitdir.getParentFile();
 		File other = new File(parent, "notagit");
-		assertEquals(gitdir, FileKey.exact(gitdir, db.getFS()).getFile());
-		assertEquals(parent, FileKey.exact(parent, db.getFS()).getFile());
-		assertEquals(other, FileKey.exact(other, db.getFS()).getFile());
+		assertEqualsFile(gitdir, FileKey.exact(gitdir, db.getFS()).getFile());
+		assertEqualsFile(parent, FileKey.exact(parent, db.getFS()).getFile());
+		assertEqualsFile(other, FileKey.exact(other, db.getFS()).getFile());
 
-		assertEquals(gitdir, FileKey.lenient(gitdir, db.getFS()).getFile());
-		assertEquals(gitdir, FileKey.lenient(parent, db.getFS()).getFile());
-		assertEquals(other, FileKey.lenient(other, db.getFS()).getFile());
+		assertEqualsFile(gitdir, FileKey.lenient(gitdir, db.getFS()).getFile());
+		assertEqualsFile(gitdir, FileKey.lenient(parent, db.getFS()).getFile());
+		assertEqualsFile(other, FileKey.lenient(other, db.getFS()).getFile());
 	}
 
 	@Test
@@ -83,10 +83,11 @@ public void testBareFileKey() throws IOException {
 		assertTrue(name.endsWith(".git"));
 		name = name.substring(0, name.length() - 4);
 
-		assertEquals(gitdir, FileKey.exact(gitdir, db.getFS()).getFile());
+		assertEqualsFile(gitdir, FileKey.exact(gitdir, db.getFS()).getFile());
 
-		assertEquals(gitdir, FileKey.lenient(gitdir, db.getFS()).getFile());
-		assertEquals(gitdir, FileKey.lenient(new File(parent, name), db.getFS()).getFile());
+		assertEqualsFile(gitdir, FileKey.lenient(gitdir, db.getFS()).getFile());
+		assertEqualsFile(gitdir,
+				FileKey.lenient(new File(parent, name), db.getFS()).getFile());
 	}
 
 	@Test
@@ -95,12 +96,12 @@ public void testFileKeyOpenExisting() throws IOException {
 
 		r = new FileKey(db.getDirectory(), db.getFS()).open(true);
 		assertNotNull(r);
-		assertEquals(db.getDirectory(), r.getDirectory());
+		assertEqualsFile(db.getDirectory(), r.getDirectory());
 		r.close();
 
 		r = new FileKey(db.getDirectory(), db.getFS()).open(false);
 		assertNotNull(r);
-		assertEquals(db.getDirectory(), r.getDirectory());
+		assertEqualsFile(db.getDirectory(), r.getDirectory());
 		r.close();
 	}
 
@@ -116,12 +117,13 @@ public void testFileKeyOpenNew() throws IOException {
 			new FileKey(gitdir, db.getFS()).open(true);
 			fail("incorrectly opened a non existant repository");
 		} catch (RepositoryNotFoundException e) {
-			assertEquals("repository not found: " + gitdir, e.getMessage());
+			assertEquals("repository not found: " + gitdir.getCanonicalPath(),
+					e.getMessage());
 		}
 
 		final Repository o = new FileKey(gitdir, db.getFS()).open(false);
 		assertNotNull(o);
-		assertEquals(gitdir, o.getDirectory());
+		assertEqualsFile(gitdir, o.getDirectory());
 		assertFalse(gitdir.exists());
 	}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java
index f44f67f84..2b9c10777 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java
@@ -221,8 +221,9 @@ public void apply(DirCacheEntry ent) {
 		Repository subRepo = gen.getRepository();
 		addRepoToClose(subRepo);
 		assertNotNull(subRepo);
-		assertEquals(modulesGitDir, subRepo.getDirectory());
-		assertEquals(new File(db.getWorkTree(), path), subRepo.getWorkTree());
+		assertEqualsFile(modulesGitDir, subRepo.getDirectory());
+		assertEqualsFile(new File(db.getWorkTree(), path),
+				subRepo.getWorkTree());
 		assertFalse(gen.next());
 	}