The 5.1 series of MySQLwas unmasked for the gentoo portage. When upgrading from an older major version (including 5.0), you will be required to rebuild everything linked to the libmysqlclient.so.15 and libmysqlclient_r.so.15. You can do this by installing app-portage/gentoolkit and running: # revdep-rebuild --library libmysqlclient.so.15 # revdep-rebuild --library libmysqlclient_r.so.15 If you use the Portage 2.2 series, you may also use: # emerge @preserved-rebuild The official upgrade documentation is available here: http://dev.mysql.com/doc/refman/5.1/en/upgrading.html Note that existing databases may need converting as well, again including those upgrading from 5.0 to 5.1.