If you want to use transactions (trust me, you want) you have to use InnoDB tables, so add default-table-type=InnoDB to your mysql configuration file (my.cnf or my.ini). This solution is Hibernate friendly.
For example in windows you can use the following my.ini in the windows dir:
[mysqld] # Uncomment the following if you want to log updates log-bin # Uncomment the following if you are NOT using BDB tables skip-bdb # Uncomment the following if you are using Innobase tables innodb_data_file_path = ibdata1:20M:autoextend default-table-type=InnoDB
If you are using a MySQL version previous to 4.0 you should check InnoDB configuration to enable InnoDB.