Most often, the internal optimizations in InnoDB described in section Section 3.4.2, “InnoDB Data Storage and Compression” ensure that the system runs well with compressed data. However, because the efficiency of compression depends on the nature of your data, there are some factors you should consider to get best performance. You need to choose which tables to compress, and what compressed page size to use. You may also want to adjust the size of the buffer pool based on run-time performance characteristics such as the amount of time the system spends compressing and uncompressing data.
This is the User’s Guide for InnoDB Plugin 1.0.6 for MySQL 5.1, generated on March 4, 2010 (rev 673:680M).