The above-described substrate transfer apparatus 2d allows the substrates W held in the common carrier SC in the horizontal attitude to be transferred and stored into the exclusive carrier in a vertical attitude. Further, in reverse order to this operation, the substrates W held in the exclusive carrier EC in the vertical attitude can be transferred and stored into the common carrier SC in a horizontal attitude. Thus, even if the substrate processing system holding and transferring the substrates W in a vertical attitude is modified to transfer the substrates W in a horizontal attitude, its substrate processing apparatus for processing the substrates W in a vertical attitude can be used with little modification by applying this substrate transfer apparatus 2d. This leads to an economical operation of the substrate processing system.