In a substrate processing apparatus, a storage device, an indexer block, a processing block and an interface block are arranged to line up in this order. The storage device includes a plurality of openers on which a carrier storing a plurality of substrates can be placed. The carrier is carried in the storage device. In the storage device, the carrier is transported among the plurality of openers by a transport device. The transport device includes first and second hands configured to be able to hold the carrier and move in a horizontal direction and a vertical direction. The second hand is provided below the first hand.