A cleaning apparatus 11 includes a cleaning bath 30 for cleaning wafers W, a wafer guide 31 moving up and down to accommodate the wafers W in the cleaning bath 30, a motor 49 for moving the wafer guide 31 up and down, an absolute encoder 33 for detecting the position of the wafer guide 31, a driver 62 and a controller 63. The absolute encoder 33 detects a rotational angle of a rotating shaft 53 of the motor 49 and outputs a detection signal to the driver 62. Based on this detection signal, the driver 62 detects the position of the wafer guide 31 and further outputs the positional information of the wafer guide 31 to the controller 63. Thus, the invention provides a transferring apparatus and a substrate processing apparatus both of which allow of easy detection of the wafer guide and further facilitate their maintenance.