Measuring actual MySQL query time
Solution 1:
Start the profiler with
SET profiling = 1;
Then execute your Query.
With
SHOW PROFILES;
you see a list of queries the profiler has statistics for. And finally you choose which query to examine with
SHOW PROFILE FOR QUERY 1;
or whatever number your query has.
What you get is a list where exactly how much time was spent during the query.
More info in the manual.
Solution 2:
The accepted Answer is becoming invalid...
SHOW PROFILE[S]
are deprecated as of MySQL 5.6.7 and will be removed in a future MySQL release. Use the Performance Schema instead; see http://dev.mysql.com/doc/refman/5.6/en/performance-schema-query-profiling.html