A method and arrangement for aligning a mask comprising a mask-pattern relative to a substrate when the mask-pattern is repeatedly and directly imaged on the substrate, gratings in the mask and gratings on the substrate (phase gratings) being employed as alignment references. The gratings in the mask are located outside the mask pattern and the phase gratings are located on the substrate outside the area where the mask-pattern is imaged. The substrate (phase) gratings are imaged on one of the mask gratings with a projection system which is also used for projecting the mask-pattern on the substrate. The image of the gratings on the grating in the mask is adjusted. Thus, a very accurate alignment can be achieved.