There is provided a technique which can prevent poor processing of successive substrates in the event of a failure of a module or a transport mechanism for transporting a substrate between modules. A substrate processing apparatus includes: a plurality of modules from which a substrate holder of a substrate transport mechanism receives a substrate; a sensor section for detecting a displacement of the holding position of a substrate, held by the substrate holder, from a reference position preset in the substrate holder; and a storage section for storing the displacement, detected when the substrate holder receives a substrate from each of the modules, in a chronological manner for each module. A failure of one of the modules or the substrate transport mechanism is estimated based on the chronological data on the displacement for each module, stored in the storage section. This enables an early detection of a failure or abnormality.