A pattern inspection method including: sequentially imaging plural chip formed on a substrate; selecting at least one of pattern sections of each inspection image obtained by the imaging, while discarding other pattern sections, based on a recipe created in advance, the recipe including information for determining which pattern sections to be selected or discarded; calculating position gap between an inspection image of a chip obtained by the imaging and a reference image stored in a memory by using positional information of pattern images included in the inspection image and reference pattern images which are both corresponding to the at least one of pattern sections selected at the selecting; aligning the inspection image and the reference image by using information of the calculated position gap; and comparing the aligned inspection image with the reference image, and extracting a difference between the two images as a defect candidate.