fsck.ext3 [options]
Better check the options, as well for manual but especially for automated use.
Many distros (e.g. slackware) would do a fsck on boot on the root fs, and the mechanism seems to be rather complex, e.g. in case of changes having to be made, an automatic reboot would be necessary; so it is a matter of scripting.
Basically you can run filesystem checks whenever, only precondition to be unmounted.