diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
index e3c225ff6..9a9940898 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
@@ -417,7 +417,13 @@ public boolean checkout() throws IOException {
 			if (!file.getParentFile().mkdirs()) {
 				// ignore
 			}
+
 			DirCacheEntry entry = dc.getEntry(path);
+
+			// submodules are handled with separate operations
+			if (FileMode.GITLINK.equals(entry.getRawMode()))
+				continue;
+
 			checkoutEntry(repo, file, entry);
 		}