In a lithographic projection apparatus, a time-saving height measurement method is used. While in a projection station (105, 108, 111) the pattern of a mask (129) is projected on the fields of a first substrate (120), the height of the fields of a second substrate (121) is measured in a measuring station (133). In the measuring station, the height of the substrate fields and the height of the substrate holder (113) are measured by a first height sensor (150) and a second height sensor (160), respectively, and the value of the height of the substrate holder associated with the ideal height of the substrate field is determined for each substrate field. In the projection station, only the height of the substrate holder (111) is controlled by a third height sensor (180). The second and third height sensors are preferably part of a composite XY interferometer system extended with a Z measuring axis.