The easy way would be to create an ASCII dump of both databases (using, for example, mysqldump) and then use a traditional diff (or Algorithm::Diff) on those files. There is a module on CPAN that allows you to do the diff between two databases by issuing select *, count(*) from $table group by *, which is quite memory intensive, but might work as well for you. Also, there is SQL::Translator::Diff, which claims to create the proper ALTER TABLE statements for you.