diff -Naurp mysql-cluster-gpl-7.1.3/mysql-test/r/symlink.result mysql-cluster-gpl-7.1.3.oden/mysql-test/r/symlink.result
--- mysql-cluster-gpl-7.1.3/mysql-test/r/symlink.result	2010-03-29 17:16:21.000000000 +0200
+++ mysql-cluster-gpl-7.1.3.oden/mysql-test/r/symlink.result	2010-05-26 13:55:19.277301020 +0200
@@ -168,4 +168,16 @@ Warning	1618	<DATA DIRECTORY> option ign
 Warning	1618	<INDEX DIRECTORY> option ignored
 DROP TABLE t1;
 SET @@SQL_MODE=@OLD_SQL_MODE;
+#
+# BUG#40980 - Drop table can remove another MyISAM table's
+#             data and index files
+#
+CREATE TABLE user(a INT) DATA DIRECTORY='MYSQL_TMP_DIR/mysql'
+                             INDEX DIRECTORY='MYSQL_TMP_DIR/mysql';
+FLUSH TABLE user;
+# Symlinking mysql database to tmpdir
+FLUSH TABLE mysql.user;
+DROP TABLE user;
+FLUSH TABLE mysql.user;
+SELECT * FROM mysql.user;
 End of 5.1 tests
diff -Naurp mysql-cluster-gpl-7.1.3/mysql-test/t/symlink.test mysql-cluster-gpl-7.1.3.oden/mysql-test/t/symlink.test
--- mysql-cluster-gpl-7.1.3/mysql-test/t/symlink.test	2010-03-29 17:15:52.000000000 +0200
+++ mysql-cluster-gpl-7.1.3.oden/mysql-test/t/symlink.test	2010-05-26 13:55:19.278300392 +0200
@@ -249,4 +249,26 @@ eval CREATE TABLE t1(a INT) DATA DIRECTO
 DROP TABLE t1;
 SET @@SQL_MODE=@OLD_SQL_MODE;
 
+--echo #
+--echo # BUG#40980 - Drop table can remove another MyISAM table's
+--echo #             data and index files
+--echo #
+--mkdir $MYSQL_TMP_DIR/mysql 
+--replace_result $MYSQL_TMP_DIR MYSQL_TMP_DIR
+eval CREATE TABLE user(a INT) DATA DIRECTORY='$MYSQL_TMP_DIR/mysql'
+                             INDEX DIRECTORY='$MYSQL_TMP_DIR/mysql';
+FLUSH TABLE user;
+--echo # Symlinking mysql database to tmpdir
+--remove_file $MYSQL_TMP_DIR/mysql/user.MYD
+--remove_file $MYSQL_TMP_DIR/mysql/user.MYI
+--rmdir $MYSQL_TMP_DIR/mysql
+--exec ln -s $MYSQLD_DATADIR/mysql $MYSQL_TMP_DIR/mysql
+FLUSH TABLE mysql.user;
+DROP TABLE user;
+FLUSH TABLE mysql.user;
+--disable_result_log
+SELECT * FROM mysql.user;
+--enable_result_log
+--remove_file $MYSQL_TMP_DIR/mysql
+
 --echo End of 5.1 tests
diff -Naurp mysql-cluster-gpl-7.1.3/storage/myisam/mi_delete_table.c mysql-cluster-gpl-7.1.3.oden/storage/myisam/mi_delete_table.c
--- mysql-cluster-gpl-7.1.3/storage/myisam/mi_delete_table.c	2010-03-29 16:51:37.000000000 +0200
+++ mysql-cluster-gpl-7.1.3.oden/storage/myisam/mi_delete_table.c	2010-05-26 13:55:19.278300392 +0200
@@ -22,6 +22,41 @@
 
 #include "fulltext.h"
 
+
+/**
+  Remove MyISAM data/index file safely
+
+  @details
+    If name is a symlink and file it is pointing to is not in
+    data directory, file is also removed.
+
+  @param name    file to remove
+  
+  @returns
+    0 on success or my_errno on failure
+*/
+
+static int _mi_safe_delete_file(const char *name)
+{
+  DBUG_ENTER("_mi_safe_delete_file");
+  if (my_is_symlink(name) && (*myisam_test_invalid_symlink)(name))
+  {
+    /*
+      Symlink is pointing to file in data directory.
+      Remove symlink, keep file.
+    */
+    if (my_delete(name, MYF(MY_WME)))
+      DBUG_RETURN(my_errno);
+  }
+  else
+  {
+    if (my_delete_with_symlink(name, MYF(MY_WME)))
+      DBUG_RETURN(my_errno);
+  }
+  DBUG_RETURN(0);
+}
+
+
 int mi_delete_table(const char *name)
 {
   char from[FN_REFLEN];
@@ -61,12 +96,12 @@ int mi_delete_table(const char *name)
 #endif /* USE_RAID */
 
   fn_format(from,name,"",MI_NAME_IEXT,MY_UNPACK_FILENAME|MY_APPEND_EXT);
-  if (my_delete_with_symlink(from, MYF(MY_WME)))
+  if (_mi_safe_delete_file(from))
     DBUG_RETURN(my_errno);
   fn_format(from,name,"",MI_NAME_DEXT,MY_UNPACK_FILENAME|MY_APPEND_EXT);
 #ifdef USE_RAID
   if (raid_type)
     DBUG_RETURN(my_raid_delete(from, raid_chunks, MYF(MY_WME)) ? my_errno : 0);
 #endif
-  DBUG_RETURN(my_delete_with_symlink(from, MYF(MY_WME)) ? my_errno : 0);
+  DBUG_RETURN(_mi_safe_delete_file(from));
 }