A substrate inspection system includes a plurality of processing units, and each processing unit is provided with a transport mechanism configured to transport an substrate to be inspected along a transport passage which extends substantially horizontally, a lift mechanism configured to lift the substrate to be inspected to a height position, at a set position on the transport passage, and processors each configured to perform a predetermined process on the substrate to be inspected positioned at the height position. The processing units are arranged such that transport passages thereof are aligned and such that the transport directions thereof are the same direction. Between two adjacent transport passages, the substrate to be inspected is delivered from the transport passage on an upstream side to the transport passage on a downstream side.