As time goes on, all the database operations performed on your WordPress tables (which are what store your blog posts and other data) will create what’s called “overhead.” To keep your database running smoothly, you can get rid of this overhead by “optimizing” your tables (similar to defragmenting your hard drive).
Here are two ways to do it.
Method 1: WP-DBManager
Download and install the WP-DBManager plugin.
The plugin allows you to, among other things, optimize your tables from within your WordPress admin (just go to the “Databases” section and click the “Optimize DB” tab), as well as schedule table optimizations on a regular basis.
However, the plugin also lets you delete tables and provides an interface for running MySQL queries, so if you don’t like the idea of all that power being vested in your WordPress admin, you can try the phpMyAdmin method instead.
Method 2: phpMyAdmin
Here are the steps for using the phpMyAdmin software.
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Go to your web hosting account’s cPanel and click the “phpMyAdmin” icon. If you don’t see one, look for a “MySQL Databases” icon, click it, scroll to the bottom of the page, and click the “phpMyAdmin” link.
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Select your WordPress database.
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Look in the “Overhead” column. If you see a table with overhead, click the overhead value.
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Click the “Optimize Table” link.
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Once it’s done, click the Back button twice (to go back to the tables list), and repeat from step 3.
And that’s it!

personally, I prefer phpmysadmin
i prefer the 2nd method,too.
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Thanks – made the process really easy!
Does the DB-manager plugin work with WP 2.6.3? I believe the DB structure has changed from 2.3.x and don’t want to make my DB problem any worse.
@Tyler: By the looks of this forum post, it appears the author of WP-DBManager has made it compatible with WordPress 2.6. But if your DB is already giving you trouble, you may want to back up the DB before using the plugin, just in case.
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OMG! Thank you. This was just the info I needed. The 2nd method was so easy.
I would suggest one edit to your instructions for Step 4. I had a devil of a time locating the “Optimize Table” link. Had to click “Details” link below the table, and found the “Optimize Table” link at the bottom of the Space usage info.
Whew!
Wow, nice and simple thanks!
Using phpMyAdmin is the easiest way to remove the overhead in database tables.
It’s kind of interesting to see that when I delete Spam comments or trash comments in bulk, the overhead suddenly increases in the wp-comments table where it should have been the opposite way.
Thanks, You saved my day! WordPress became too slow after few days. i had to truncate few counter tables beside optimizing them.. thanks once again…