In a method of detecting defects in patterns and an apparatus for performing the method, a first image of a detection region on a semiconductor substrate may be acquired. A second image may be acquired from the first image by performing a Fourier transform and performing a low pass filtering. The second image may be compared with a reference image so that the defects of the detection region are detected. Existence of the defect of the second image is determined using a relation value between a grey level of each of pixels of the second image and the reference image, respectively. When a defect exists, the horizontal and the vertical positions of the pixel where the relation value is minimum are combined to determine the position of the defect.