A substrate processing apparatus includes: a load port into which the transport container is carried; a detecting unit that detects storage condition of the substrates which are contained in the transport container, which has been carried into the load port and the lid of which has been removed; a processing unit that processes the substrates removed from the transport container having been carried into the load port; and a control unit. The control unit performs a first step that detects storage condition of the substrates, which are contained in the transport container having been carried into the load port, before the substrates are removed from the transport container to be delivered to the processing unit; a second step that detects storage condition of the substrates, which have been processed in the processing unit and returned to the original transport container, before closing the lid; and a third step that judges whether or not the transport container has an abnormality based on results of the first and second steps.