A pattern inspection method and apparatus are provided for sequentially imaging plural chips formed on a substrate to be inspected to and obtaining inspection images and reference images, calculating a position gap between the inspection images and the reference images using a recipe created in advance by using another substrate of the same kind or type as the substrate, the recipe including information for determining which pattern sections are to be selected and discarded, aligning the inspection images and the reference images using information of the position gap from the calculating step, and comparing the inspection images with the reference images aligned by the aligning step and extracting a defect candidate.