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.