An alignment system uses a self-referencing interferometer that produces two overlapping and relatively rotated images of an alignment markers. Detectors detect intensities in a pupil plane where Fourier transforms of the images are caused to interfere. The positional information is derived from the phase difference between diffraction orders of the two images which manifests as intensity variations in the interfered orders. Asymmetry can also be measured by measuring intensities at two positions either side of a diffraction order.