A pattern inspection apparatus including: an image detecting part for detecting a digital image of an object substrate; a display having a screen on which the digital image of the object substrate and/or a distribution of defect candidates in a map form are displayable; an input device for inputting information of a non-inspection region to be masked on the object substrate by defining a region on the screen on which said distribution of defect candidates is displayed in a map form; a memory part for storing coordinate data, pattern data or feature quantity data of the non-inspection region to be masked on the object substrate inputted on the screen by the input device; and a defect judging part in which the digital image detected by the image detecting part is examined in a state that a region matching with a condition stored in the memory part is masked and a defect is detected in a region other than said masked region.