In order to perform a measurement operation of a pattern and a processing operation in parallel while the positions of two substrate stages are accurately measured and wire/hose units are prevented from becoming tangled, a substrate processing apparatus includes an alignment system for measuring the pattern arrangements of the substrates, a processing system disposed separately from the alignment system and used for processing the substrates, substrate stages which are able to support the substrates and move in an xy plane, and position measurement systems which measure the positions of the substrate stages. Four position measurement systems are arranged for the measurement in the x direction, and three position measurement systems are arranged for the measurement in the y direction. One of the position measurement systems for the measurement in the y direction is disposed at a side opposite to the remaining positioning measurement systems across the substrate stages.