MySQL uses the value of the TMPDIR environment variable as the pathname of the directory in which to store temporary files. If you don't have TMPDIR set, MySQL uses the system default, which is normally /tmp, /var/tmp, or /usr/tmp. If the filesystem containing your temporary file directory is too small, you can use the --tmpdir option to mysqld to specify a directory in a filesystem where you have enough space.

In MySQL 5.1, the --tmpdir option can be set to a list of several paths that are used in round-robin fashion. Paths should be separated by colon characters (‘:’) on Unix and semicolon characters (‘;’) on Windows, NetWare, and OS/2. Note: To spread the load effectively, these paths should be located on different physical disks, not different partitions of the same disk.

If the MySQL server is acting as a replication slave, you should not set --tmpdir to point to a directory on a memory-based filesystem or to a directory that is cleared when the server host restarts. A replication slave needs some of its temporary files to survive a machine restart so that it can replicate temporary tables or LOAD DATA INFILE operations. If files in the temporary file directory are lost when the server restarts, replication fails.

MySQL creates all temporary files as hidden files. This ensures that the temporary files are removed if mysqld is terminated. The disadvantage of using hidden files is that you do not see a big temporary file that fills up the filesystem in which the temporary file directory is located.

MySQL Enterprise.  Advisors provided by the MySQL Network Monitoring and Advisory Service automatically detect excessive temporary table storage to disk. For more information see, http://www.mysql.com/products/enterprise/advisors.html.

When sorting (ORDER BY or GROUP BY), MySQL normally uses one or two temporary files. The maximum disk space required is determined by the following expression:

(length of what is sorted + sizeof(row pointer))
* number of matched rows
* 2

The row pointer size is usually four bytes, but may grow in the future for really big tables.

For some SELECT queries, MySQL also creates temporary SQL tables. These are not hidden and have names of the form SQL_*.

ALTER TABLE creates a temporary table in the same directory as the original table.