In a substrate processing apparatus comprising a processing unit where a specific type of processing is executed on a wafer and a transfer chamber through which a wafer is carried into/out of the processing unit, the transfer chamber includes an air intake unit through which external air is drawn into the transfer chamber, a discharge unit disposed so as to face opposite the air intake unit, through which the discharge gas in the transfer chamber is discharged and a discharge gas filtering means disposed at the discharge unit and constituted with a harmful constituent eliminating filter through which a harmful constituent contained in the discharge gas, at least, is eliminated.