From the yum manual:
«CLEAN OPTIONS
The following are the ways which you can invoke yum in clean mode.
yum clean packages
Eliminate any cached packages from the system. Note that pack-
ages are not automatically deleted after they are downloaded.
yum clean headers
Eliminate all of the files which yum uses to determine the
remote availability of packages. Using this option will force
yum to download all the headers the next time it is run.
yum clean all
Runs yum clean packages and yum clean headers as above.»
The «yum clean all» command will not only remove cached packages, but also any headers. i do it occasionally to totally flush out everything in case there are obsolete headers – which can also take up space, albeit not very much. The reason it takes a little longer next time you run «yum update» is because that cache of headers needs to be replenished. Run «yum clean packages» next time, and you can avoid this extra wait, because the headers will still be cached on your box.