A substrate processing apparatus comprises a storage container for storing multiple substrates and whose substrate loading and unloading opening is shut by a lid, a loading and unloading port for carrying the storage container into and out of the case, a placement unit for placing the storage container in the loading and unloading port, a storage chamber provided adjacent to the loading and unloading port for storing the storage container, an opening and closing device for opening and closing the substrate loading and unloading opening of the storage container placed in the placement unit, a transfer device containing a holding mechanism for supporting the bottom of the storage container and transferring the storage container supported in the holding mechanism, over the opening and closing device between the inside and outside of the storage chamber, and an elevator mechanism for raising and lowering the placement unit between the placement unit height position where the opening and closing device opens and closes the storage container, and a height position where the transfer device gives and receives the storage container.