A lithographic apparatus comprises a substrate table to hold a substrate, a reference structure and a measurement system to measure a position of the substrate table with respect to the reference structure. The measurement system comprises a first measurement system to measure a position of the substrate table with respect to an intermediate structure and a second measurement system to measure a position of the intermediate structure with respect to the reference structure. The intermediate structure may be connected or connectable to a drive mechanism to drive the substrate table. A distance between the substrate table and the intermediate structure, resp. a distance between the intermediate structure and the reference structure may be small which results in a highly accurate position measurement.