diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
index f2ac9456d..57345e20d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
@@ -154,7 +154,7 @@ class RebuildRefTree extends TextBuiltin {
 		}
 
 		for (Ref r : refdb.getRefs(RefDatabase.ALL).values()) {
-			if (r.getName().equals(txnCommitted)
+			if (r.getName().equals(txnCommitted) || r.getName().equals(HEAD)
 					|| r.getName().startsWith(txnNamespace)) {
 				continue;
 			}