In a pattern inspection method, a master pattern serving as a reference and the continuous tone image of a pattern to be measured that is sensed by a camera are aligned. At least the position of a base in the continuous tone image of the pattern to be measured is detected on the basis of the master pattern. At least one threshold is set on the basis of the difference from at least the density value of the base. The continuous tone image of the pattern to be measured is binarized on the basis of the set threshold. The pattern to be measured is inspected by comparing the binarized pattern to be measured and the master pattern. A pattern inspection apparatus and alignment method are also disclosed.