Position sensor system for substrate transfer robot

A substrate processing apparatus comprises a substrate handling chamber, a pair of position sensors, and a substrate transfer robot. Each of the sensors comprises an emitter configured to emit a beam of light, and a receiver configured to receive the light beam. The substrate transfer robot comprises an end effector and a robot actuator. The end effector is configured to hold a substrate such that the substrate has a same expected position with respect to the end effector every time the substrate is held. The robot actuator is configured to move the end effector within the handling chamber to transfer substrates among a plurality of substrate stations. An edge of a substrate held in the expected position by the end effector can partially block a light beam of one of the position sensors, while another end of the end effector partially blocks a light beam of the other position sensor.