(mysql.info) innodb-file-defragmenting

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 14.2.14.3 Defragmenting a Table
 ...............................
 
 If there are random insertions into or deletions from the indexes of a
 table, the indexes may become fragmented.  Fragmentation means that the
 physical ordering of the index pages on the disk is not close to the
 index ordering of the records on the pages, or that there are many
 unused pages in the 64-page blocks that were allocated to the index.
 
 A symptom of fragmentation is that a table takes more space than it
 `should' take. How much that is exactly, is difficult to determine. All
 `InnoDB' data and indexes are stored in B-trees, and their fill factor
 may vary from 50% to 100%. Another symptom of fragmentation is that a
 table scan such as this takes more time than it `should' take:
 
      SELECT COUNT(*) FROM t WHERE a_non_indexed_column <> 12345;
 
 (In the preceding query, we are `fooling' the SQL optimizer into
 scanning the clustered index, rather than a secondary index.) Most
 disks can read 10 to 50MB/s, which can be used to estimate how fast a
 table scan should run.
 
 It can speed up index scans if you periodically perform a `null' `ALTER
 TABLE' operation:
 
      ALTER TABLE TBL_NAME ENGINE=INNODB
 
 That causes MySQL to rebuild the table. Another way to perform a
 defragmentation operation is to use `mysqldump' to dump the table to a
 text file, drop the table, and reload it from the dump file.
 
 If the insertions to an index are always ascending and records are
 deleted only from the end, the `InnoDB' filespace management algorithm
 guarantees that fragmentation in the index does not occur.
 

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