Answer by Cyno for How to shrink/purge ibdata1 file in MySQL

If your goal is to monitor MySQL free space and you can't stop MySQL to shrink your ibdata file, then get it through table status commands. Example:

MySQL > 5.1.24:

mysqlshow --status myInnodbDatabase myTable | awk '{print $20}'

MySQL < 5.1.24:

mysqlshow --status myInnodbDatabase myTable | awk '{print $35}'

Then compare this value to your ibdata file:

du -b ibdata1

Source: http://dev.mysql.com/doc/refman/5.1/en/show-table-status.html