Hi Maxoq,
This is a common problem with MySQL using InnoDB.
ibdata1, holds ALL the data from EVERY InnoDB table you have on your MySQL server.
This file never shrinks in size, it only expands to contain new data.
One way of fixing this issue is having MySQL keep data tables in their own files.
Export/dump all your databases.
Drop all databases, except for the mysql database, and information_schema, if it exists.
Shut down MySQL.
Delete the ibdata1 file and any ib_logfile log files.
Add innodb_file_per_table under the [mysqld] heading in your my.cnf file.
Start MySQL.
Import all your databases.
This should result in less disk usage with the new configuration.
Warning: As you can see this a major change and I would advise you are sure about making any changes before doing so.
