A pattern inspection apparatus which compares images of regions, corresponding to each other, of patterns that are formed so as to be identical and judges that non-coincident portions in the images are defects. The pattern inspection apparatus is equipped with an image comparing section which plots individual pixels of an inspection subject image in a feature space and detects excessively deviated points in the feature space as defects. Defects can be detected correctly even when the same patterns in images have a brightness difference due to a difference in the thickness of a film formed on a wafer.