A pattern inspection apparatus configured to perform pattern inspection based on a SEM image previously measures distortion amount data representing a magnitude distribution of positional displacement caused by distortion of the SEM image in a scanning direction. When the pattern inspection is performed, the apparatus makes design data and the SEM image correspond to each other by adjusting at least one of the design data and the SEM image on the basis of the distortion amount data, and places a measurement region on the SEM image on the basis of a correspondence between the design data and the SEM image. The apparatus may further find a matching rate between a pattern of the design data and a pattern of the SEM image.