MySQL recently fixed a known bug (I was not aware of this before) of OPTIMIZE TABLE (in MySQL Server 5.1.55, 5.5.9) in which OPTIMIZE TABLE statement was not preserving the AUTO_INCREMENT counter on OPTIMIZE TABLE operation.

Want to see yourself? Lets do it (code taken from the MySQL bug report)

CREATE TABLE a (a INTEGER PRIMARY KEY NOT NULL AUTO_INCREMENT) ENGINE=INNODB;
 
INSERT INTO a VALUES ();
INSERT INTO a VALUES ();
INSERT INTO a VALUES ();
 
DELETE FROM a ;
 
SHOW TABLE STATUS LIKE 'a';

In the below table status, you can see the AUTO_INCREMENT value is 4 (even after deleting all the rows which is normal behavior).

mysql> SHOW TABLE STATUS LIKE 'a'\G
*************************** 1. row ***************************
           Name: a
         Engine: InnoDB
        Version: 10
     Row_format: Compact
           Rows: 3
 Avg_row_length: 5461
    Data_length: 16384
Max_data_length: 0
   Index_length: 0
      Data_free: 4194304
 Auto_increment: 4
    Create_time: 2011-02-20 07:52:18
    Update_time: NULL
     Check_time: NULL
      Collation: latin1_swedish_ci
       Checksum: NULL
 Create_options:
        Comment:
1 row in set (0.00 sec)

Now execute the OPTIMIZE TABLE command and check the table status

OPTIMIZE TABLE a;
 
SHOW TABLE STATUS LIKE 'a';

mysql> SHOW TABLE STATUS LIKE 'a'\G
*************************** 1. row ***************************
           Name: a
         Engine: InnoDB
        Version: 10
     Row_format: Compact
           Rows: 0
 Avg_row_length: 0
    Data_length: 16384
Max_data_length: 0
   Index_length: 0
      Data_free: 4194304
 Auto_increment: 1
    Create_time: 2011-02-20 07:52:18
    Update_time: NULL
     Check_time: NULL
      Collation: latin1_swedish_ci
       Checksum: NULL
 Create_options:
        Comment:
1 row in set (0.00 sec)

MySQL fixed this bug 5 years after the bug report.

So be careful with OPTIMIZE TABLE if you have older MySQL versions.

TRUNCATE TABLE reset the AUTO_INCREMENT to 1 so don't confuse this example with TRUNCATE TABLE.