Once your data reaches a stable size, or a growing table has increased by tens or some hundreds of megabytes, consider using the OPTIMIZE TABLE statement to reorganize the table and compact any wasted space. The reorganized tables require less disk I/O to perform full table scans. This is a straightforward technique that can improve performance when other techniques such as improving index usage or tuning application code are not practical.

OPTIMIZE TABLE copies the data part of the table and rebuilds the indexes. The benefits come from improved packing of data within indexes, and reduced fragmentation within the tablespaces and on disk. The benefits vary depending on the data in each table. You may find that there are significant gains for some and not for others, or that the gains decrease over time until you next optimize the table. This operation can be slow if the table is large or if the indexes being rebuilt don't fit into the buffer pool. The first run after adding a lot of data to a table is often much slower than later runs.

In InnoDB, having a long PRIMARY KEY (either a single column with a lengthy value, or several columns that form a long composite value) wastes a lot of disk space. The primary key value for a row is duplicated in all the secondary index records that point to the same row. (See Section 13.6.11, “InnoDB Table and Index Structures”.) Create an AUTO_INCREMENT column as the primary key if your primary key is long, or index a prefix of a long VARCHAR column instead of the entire column.

Use the VARCHAR data type instead of CHAR to store variable-length strings or for columns with many NULL values. A CHAR(N) column always takes N characters to store data, even if the string is shorter or its value is NULL. Smaller tables fit better in the buffer pool and reduce disk I/O.

When using COMPACT row format (the default InnoDB format in MySQL 5.5) and variable-length character sets, such as utf8 or sjis, CHAR(N) columns occupy a variable amount of space, but still at least N bytes.

For tables that are big, or contain lots of repetitive text or numeric data, consider using COMPRESSED row format. Less disk I/O is required to bring data into the buffer pool, or to perform full table scans. Before making a permanent decision, measure the amount of compression you can achieve by using COMPRESSED versus COMPACT row format.