In an embodiment of a method of inspecting a substrate, the substrate on which minute structures are formed is divided into a plurality of inspection regions. A main inspection region among the inspection regions is selected. A main image of the main inspection region and sub-images of sub-inspection regions adjacent to the main inspection region are obtained. An average image of the main image and the sub-images is obtained. The average image is then compared with the main image to detect defects in the main inspection region. Gray levels may be used. The average image may have improved quality so that the defects in the selected inspection region may be rapidly and accurately detected. This process has an improved reliability. Further, the number of inspecting processes for the substrate may be reduced. And a line for the inspection process may be automated so that a worker-free line may be established.