A lithographic apparatus includes a system to compensate for the effect of thermal distortion of the substrate table on position measurements of the substrate table using lateral mirrors in the substrate table. Methods of calibrating a lithographic apparatus using various substrate table scan trajectories and measurements of the localized position and rotation of lateral mirrors in the substrate table are presented. A dual stage lithographic apparatus with alignment marks defining the geometry of a lateral mirror used only at the exposure station to measure the geometry of the lateral mirror when the substrate table is at the measurement station.