Mohsen,
   First off, what version of MySQL are you running and on what platform?
Now when i use --skip-grant-tables i can see my databases.
Please help me...
When you use MySQL via a shell I would assume you're logging in as root? You also say you can only see a "test" database, can you not see a "mysql" database there as well? I would suggest that somehow either the "mysql" database has been dropped/destroyed or perhaps just the db, host, tables_priv, and user tables of that database have been dropped/destroyed/messed up.

Log in via shell and show us the result of the following commands...
"
mysql> use mysql;
mysql> show tables;
mysql> SELECT COUNT(*) FROM db;
mysql> SELECT COUNT(*) FROM user;
"

If you can't see the database and/or the tables I'm talking about you may want to just check your backups are working and come back to us.

Regards,
   Phil

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