A method of measuring a phase difference between two regions in an aberration function: Reference structures are produced on a substrate using illumination that minimizes effects of phase aberration. A grating is produced on the substrate using a phase-shift grating reticle to produce, in the exit pupil, a pair of diffracted non-zero orders, while forbidding other diffracted orders and produces interference fringes formed by interference between the pair. The interference contributes to a first grating on the substrate. Overlay error is measured between the grating and the reference structure using diffraction-based or image-based overlay measurements. A phase aberration function for the exit pupil of the lithographic apparatus can then be determined from the measured overlay errors.