From MySQL version 4.0, InnoDB is enabled by default. The following information only applies to the 3.23 series.
InnoDB tables are included in the MySQL source distribution starting from 3.23.34a and are activated in the MySQL -Max binary of the 3.23 series. For Windows, the MySQL-Max binaries are included in the standard distribution.
If you have downloaded a binary version of MySQL that includes support for InnoDB, simply follow the instructions of the MySQL manual for installing a binary version of MySQL. If you already have MySQL-3.23 installed, then the simplest way to install MySQL -Max is to replace the server executable mysqld with the corresponding executable in the -Max distribution. MySQL and MySQL -Max differ only in the server executable. See Installing binary. See mysqld-max.
To compile MySQL with InnoDB support, download MySQL-3.23.34a or newer version from http://www.mysql.com/ and configure MySQL with the --with-innodb option. See the MySQL manual about installing a MySQL source distribution. See Installing source.
cd /path/to/source/of/mysql-3.23.37 ./configure --with-innodb
To use InnoDB tables in MySQL-Max-3.23 you must specify configuration parameters in the [mysqld] section of the configuration file my.cnf, or on Windows optionally in my.ini.
At the minimum, in 3.23 you must specify innodb_data_file_path where you specify the names and the sizes of datafiles. If you do not mention innodb_data_home_dir in my.cnf the default is to create these files to the datadir of MySQL. If you specify innodb_data_home_dir as an empty string, then you can give absolute paths to your datafiles in innodb_data_file_path.
The minimal way to modify it is to add to the [mysqld] section the line
innodb_data_file_path=ibdata:30M
but to get good performance it is best that you specify options as recommended. See InnoDB start.