A lithographic apparatus includes a positioner configured to position a first part of the apparatus relative to a second part of the apparatus, the positioner including a motor having a motor position dependent motor constant defining a relation between a motor input and a motor output, and a control system to drive the motor, the control system including a set-point generator to provide a reference signal based on a desired position of the first part relative to the second part, and a controller to provide a drive signal to the motor based on the reference signal, wherein the controller includes a compensator which is configured to at least partially compensate the drive signal for the motor position dependent motor constant. The invention further relates to a positioner, a method to optimize the positioning system, and a method to derive a motor position dependent motor constant.