In this way, the substrates W cleaned in the substrate processing unit 3 are returned again to the pushing-out part 25 and stored in the common carrier SC placed on the carrier placing stage 221 in reverse order to how the substrates W are transferred from the carrier placing unit 2 to the substrate processing unit 3. More specifically, the substrates W are stored in the exclusive carrier EC in the vertical attitude at the pushing-out part 25; the exclusive carrier EC is transported to the turning part 23 by the exclusive carrier transport robot 24; the exclusive carrier EC turns from the vertical attitude to a horizontal attitude together with the substrates W at the turning part 23; and the substrates W held in the exclusive carrier EC are transferred into the common carrier SC placed on the common carrier placing part 22 by the substrate transfer robot 21. By this time, the common carrier SC has been replaced by another common carrier SC for storing the cleaned substrates W by performing the transfer of the common carrier SC into and out of the apparatus while the substrates W are cleaning.