diff --git a/sha1_file.c b/sha1_file.c
index 06c809aeeb..dae6433c06 100644
--- a/sha1_file.c
+++ b/sha1_file.c
@@ -303,7 +303,8 @@ static int link_alt_odb_entry(const char *entry, const char *relative_base, int
 	 * thing twice, or object directory itself.
 	 */
 	for (alt = alt_odb_list; alt; alt = alt->next) {
-		if (!memcmp(ent->base, alt->base, pfxlen)) {
+		if (pfxlen == alt->name - alt->base - 1 &&
+		    !memcmp(ent->base, alt->base, pfxlen)) {
 			free(ent);
 			return -1;
 		}