A registration detection system realizes both substrate-by-substrate correction and highly accurate correction of an exposure process. Therefore, the registration detection system includes: the first detection apparatus installed on a pathway to a collection in a transport container of substrates taken out of the transport container, after passing at least an exposure process and a development process, registration-detects the substrates after passing the development process at multiple points; the second detection apparatus outside the pathway, and performing registration-detecting the substrates at more points than the first detection apparatus when the substrates after passing the first detection apparatus and collected in the transport container are taken out from the transport container again; and a generation unit (image processing parts of the aforementioned detection apparatuses) that generates compensation data for the exposure process based on detection results by the first detection apparatus and detection results by the second detection apparatus.