Substrate inspection apparatus, in which the acquisition of the inspection data for a defect and the acquisition of the focus data of the objective lens are performed in parallel, includes an autofocus apparatus for controlling position of the objective lens along its optical axis. The autofocus apparatus includes a focus error detection unit and a focus control signal generation unit for generating a focus control signal for controlling the position of the objective lens for each scan line using a focus data signal composed of an objective position signal or the objective position signal to which a focus error signal is added. When “i” is assumed as a positive integer and “m” is as a natural number, the focus data signal which was acquired during the scanning period of i-th scan line is used to produce the focus control signal used to scan the (i+2m)-th scan line.