Focus performance of a lithographic apparatus is measured using pairs of targets that have been exposed (1110) with an aberration setting (e.g. astigmatism) that induces a relative best focus offset between them. A calibration curve (904) is obtained in advance by exposing similar targets on FEM wafers (1174, 1172). In a set-up phase, calibration curves are obtained using multiple aberration settings, and an anchor point (910) is recorded, where all the calibration curves intersect. When a new calibration curve is measured (1192), the anchor point is used to produce an adjusted updated calibration curve (1004′) to cancel focus drift and optionally to measure drift of astigmatism. Another aspect of the disclosure (FIGS. 13-15) uses two aberration settings (+AST, −AST) in each measurement, reducing sensitivity to astigmatism drift. Another aspect (FIGS. 16-17) uses pairs of targets printed with relative focus offsets, by double exposure in one resist layer.