1. A method of detecting defects, the method including: acquiring a first image of a detection region on a semiconductor substrate; acquiring a second image from the first image by performing a Fourier transform, which transforms a two-dimensional domain to a frequency domain, and performing a low pass filtering, which preserves a low frequency domain among the frequency domain and reduces a high frequency domain among the frequency domain; and detecting the defects in the detection region by comparing the second image with a reference image; wherein detecting the defects in the detection region includes determining whether the defects of the second image exist or not; and determining positions of the defects when the defects of the second image exist, and wherein determining whether the defects of the second image exists or not includes calculating relation values between a grey level of pixels in the second image and a grey level of pixels in the reference image with respect to horizontal positions and vertical positions of pixels in the second image and the pixels in the reference image; determining that the defect does not exist in the second image when the relation values with respect to the horizontal positions of the pixels and the relation values with respect to the vertical positions of the pixels are larger than a relation value; and determining that the defect exists in the second image when at least one among the relation values with respect to the horizontal positions of the pixels and the relation values with respect to the vertical positions of the pixels is smaller than the relation value.