A substrate cleaning apparatus does not need positioning of a transport system on start-up of the apparatus and can reduce the installation area of the apparatus. The substrate cleaning apparatus includes a base-integrated frame (1) in which are mounted a substrate transport device (2) for transporting a substrate, at least one substrate processing unit (3) for processing the substrate, a substrate loading port (5) for placing a substrate-housing cassette (4) on it, and a processing liquid supply apparatus (6) for supplying a processing liquid to the substrate processing unit, wherein maintenance of the substrate processing unit (3) can be performed from the backside of the apparatus.