A method of detecting positions of first and second marks, at least one of the first and second marks being associated with a substrate, and exposing the substrate to a pattern. The method includes steps of sensing an image of the first and second marks, an image of the first mark and an image of the second mark having respective periodic patterns, of which periods are different from each other, and being formed in respective regions separate from each other, performing an orthogonal transform of a signal of the sensed image to obtain frequency components corresponding to the first and second marks, calculating positions of the first and second marks based on phases of respective frequency components corresponding to the first and second marks in the transformed signal, and positioning the substrate based on the calculated positions to expose the positioned substrate to a pattern.